[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTLIHC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/10006007/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/10013771/transformed.cor.cli.txt"

nPatients in clinical file=176, in cluster file=208, common to both=160
[1]  80 160
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               24               136 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               24               136 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               91                69 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               91                69 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               24               136 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               24               136 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               20               140 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               20               140 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               15               145 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               15               145 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               17               143 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               17               143 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               147 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               147 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               156 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               156 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               62                98 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               62                98 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               48               112 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               48               112 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               44               116 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               44               116 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               24               136 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               24               136 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               50               110 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               50               110 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               51               109 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               51               109 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               35               125 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               35               125 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               83                77 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               83                77 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7               153 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7               153 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7               153 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7               153 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                23                137 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                23                137 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                147 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                147 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                11                149 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                11                149 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                149 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                149 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                17                143 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                17                143 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                139 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                139 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                152 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                152 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                151 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                151 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                145 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                145 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                145 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                145 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                153 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                153 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                14                146 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                14                146 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                42                118 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                42                118 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                150 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                150 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                151 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                151 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                32                128 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                32                128 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                37                123 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                37                123 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                48                112 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                48                112 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                50                110 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                50                110 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                14                146 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                14                146 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                141 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                141 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               28               132 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               28               132 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               38               122 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               38               122 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13               147 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13               147 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               146 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               146 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15               145 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15               145 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22               138 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22               138 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13               147 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13               147 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               35               125 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               35               125 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               53               107 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               53               107 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               149 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               149 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               15               145 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               15               145 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17               143 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17               143 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               47               113 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               47               113 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               152 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               152 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               149 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               149 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               76                84 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               76                84 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               16               144 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               16               144 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               48               112 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               48               112 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50               110 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50               110 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                20                140 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                20                140 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                34                126 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                34                126 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                27                133 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                27                133 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                28                132 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                28                132 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                27                133 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                27                133 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                16                144 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                16                144 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                56                104 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                56                104 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                49                111 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                49                111 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                33                127 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                33                127 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                46                114 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                46                114 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                57                103 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                57                103 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                79                 81 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                79                 81 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                21                139 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                21                139 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                31                129 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                31                129 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                33                127 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                33                127 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                17                143 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                17                143 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                148 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                148 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                10                150 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                10                150 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                154 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                154 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                44                116 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                44                116 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                36                124 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                36                124 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               22               138 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               22               138 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 160 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
          NA          849           NA           NA           NA           NA 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
          NA         1351          421            8          680          289 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BW-A5NQ TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
         444          387           NA            2           NA           12 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
          NA           NA           NA           NA            3            2 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
           3            4         2425           NA           NA           NA 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
        3437           NA           79           NA          662           NA 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
          NA         2415         2017          602         2301          204 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
          NA           NA         1495          183          887           NA 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
          NA           NA           NA         1008          989         2232 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
         428          433          561          458           NA         1711 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
          NA         2245         2849           NA           NA           NA 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
        2018          334           NA          230          334           44 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
         843         3071          408          386          482          423 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
         406            7            6            6            6            6 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
           6            6          570          608          357          334 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
          NA          303          363           NA           NA          987 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
          NA           NA          848           NA           NA            4 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
           1           10         1836           12           37         1553 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        1636          860          935         1779           NA          655 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
         673          780          180          594          585          447 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
         364          243          133          236          182           NA 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
          NA           NA          122           NA          360          407 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
          15          291          155          433          391          265 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
          52           NA          498          135 
Variable 1:'AGE':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=87,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
 [3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
 [5] "PATHOLOGY.M.STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL.TYPE"         "COMPLETENESS.OF.RESECTION"
 [9] "RACE"                      "ETHNICITY"                
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 160 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
68 41 42  8 
[1] "table(vv)"
vv
T1 T2 T3 T4 
68 41 42  8 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
68 41 42  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
68 41 42  8 
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   14  9
  1P GAIN WILD-TYPE 77 57
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               23               134 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                9                57 
$`1P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-CC-5262 TCGA-DD-A114 
       37.32        27.52         2.99        44.42         3.39        37.78 
TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-ED-A459 
        2.60        45.11         5.62        18.44        15.06        13.41 
TCGA-ED-A4XI TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S TCGA-ES-A2HT TCGA-G3-A25W 
       12.69         0.20        18.74        19.99        14.40        30.74 
TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-MI-A75G 
       19.53        11.97         1.84        13.38        14.24 

$`1P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X 
       48.99        27.91        10.13        46.78        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57         5.03        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       22.36         9.50        14.60        12.72         0.07         2.86 
TCGA-CC-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        14.07        14.24        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
      100.96        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20         0.20         0.20        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         9.96        11.93        22.85        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-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-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       19.23        14.70         7.99         4.37         7.76         5.98 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG 
        1.02         2.66         4.01         2.14        11.84         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57         5.10        12.85         8.71         1.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.20              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            45.11            113.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            14.40             13.81 
[1] "0.2 - 45.1 (14.4)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P GAIN MUTATED         8        9         0          1          2          1
  1P GAIN WILD-TYPE      57       28         2         30          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P GAIN MUTATED          0         0         0
  1P GAIN WILD-TYPE        1         1         2
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  8                57
  STAGE II                 9                28
  STAGE III                0                 2
  STAGE IIIA               1                30
  STAGE IIIB               2                 3
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1P GAIN MUTATED    8 11  3  2
  1P GAIN WILD-TYPE 60 30 39  6
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               8                60
  T2              11                30
  T3               3                39
  T4               2                 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"
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   11  0
  1P GAIN WILD-TYPE 91  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     11    0
  1P GAIN WILD-TYPE   91    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              11                91
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1P GAIN MUTATED    16   0   8
  1P GAIN WILD-TYPE 104   3  29
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              16               104
  M1               0                 3
  MX               8                29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    5 19
  1P GAIN WILD-TYPE 55 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5   19
  1P GAIN WILD-TYPE   55   81
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               5                55
  MALE                19                81
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1P GAIN MUTATED                         0                       24
  1P GAIN WILD-TYPE                       2                      132
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1P GAIN MUTATED                                  0
  1P GAIN WILD-TYPE                                2
D1V8, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      24               132
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    18   3   0   1
  1P GAIN WILD-TYPE 113   8   1  11
D1V9, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              18               113
  R1               3                 8
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  1     6
  1P GAIN WILD-TYPE                                0    30
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           4    13
  1P GAIN WILD-TYPE                         4    96
D1V10, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          6                30
  BLACK OR AFRICAN AMERICAN                      4                 4
  WHITE                                         13                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"
D1V11, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  22
  1P GAIN WILD-TYPE   3 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   22
  1P GAIN WILD-TYPE    3  121
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              22               121
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   49 40
  1Q GAIN WILD-TYPE 42 26
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               89                68 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               40                26 
$`1Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A112 
       37.32        10.13        27.52         2.99        23.34         5.03 
TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5261 TCGA-CC-5262 
       44.42        22.36        14.60        12.72         0.39         3.39 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 
        0.07         0.13        79.73        37.78       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE 
        2.60        21.76        51.29        90.71        79.40         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-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A8 
        5.62        19.76        25.81        17.59        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.61        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73D TCGA-DD-A73G 
       29.56        73.81        12.26         0.30        10.98       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.41        12.69        13.35         0.23         0.20         0.20 
TCGA-ED-A7XP 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-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
        9.96        14.40        19.10         8.12         0.13         0.03 
TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
        1.22        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M9 
       19.53        19.23        14.70         7.99         4.37         1.84 
TCGA-HP-A5MZ TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        2.66         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-O8-A75V 
        5.10        14.24        12.85         8.71         4.44 

$`1Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Z 
       48.99        27.91        46.78        27.52        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 
       69.57        13.84         0.26         9.50         0.07         2.86 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A116 
        4.24         3.32         0.10         0.10        83.57        53.33 
TCGA-DD-A11B TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ 
        0.46        66.31        19.79        75.65         6.02        29.16 
TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       55.69         7.66        70.06        20.12       102.74       107.11 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS 
       33.14        32.52        73.38        56.25        93.67        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       66.35        10.98         9.30         7.56         1.45        27.72 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A3RK 
       15.85        13.91         0.20         0.20         0.20        11.93 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP 
       22.85        32.45        27.88         6.38         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI 
        0.39        51.06        53.79        28.27        25.64         5.92 
TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-MR-A8JO 
       11.97         7.76         5.98         1.02         4.01         1.71 
TCGA-NI-A4U2 TCGA-NI-A8LF 
       58.88        16.37 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           113.00            107.11 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            13.41             18.08 
[1] "0.0 - 113.0 (13.4)" "0.1 - 107.1 (18.1)"
[1] "hr=" "1.7"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED        34       29         1         10          4          2
  1Q GAIN WILD-TYPE      31        8         1         21          1          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q GAIN MUTATED          1         0         2
  1Q GAIN WILD-TYPE        0         1         0
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 34                31
  STAGE II                29                 8
  STAGE III                1                 1
  STAGE IIIA              10                21
  STAGE IIIB               4                 1
  STAGE IIIC               2                 3
  STAGE IV                 1                 0
  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                T1 T2 T3 T4
  1Q GAIN MUTATED   34 32 18  6
  1Q GAIN WILD-TYPE 34  9 24  2
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              34                34
  T2              32                 9
  T3              18                24
  T4               6                 2
[1] 4 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   57  0
  1Q GAIN WILD-TYPE 45  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     57    0
  1Q GAIN WILD-TYPE   45    3
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              57                45
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED   67  3 21
  1Q GAIN WILD-TYPE 53  0 16
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              67                53
  M1               3                 0
  MX              21                16
[1] 3 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   30 61
  1Q GAIN WILD-TYPE 30 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     30   61
  1Q GAIN WILD-TYPE   30   39
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              30                30
  MALE                61                39
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1Q GAIN MUTATED                         0                       90
  1Q GAIN WILD-TYPE                       2                       66
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1Q GAIN MUTATED                                  1
  1Q GAIN WILD-TYPE                                1
D2V8, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      90                66
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED   76  6  1  5
  1Q GAIN WILD-TYPE 55  5  0  7
D2V9, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              76                55
  R1               6                 5
  R2               1                 0
  RX               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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1    22
  1Q GAIN WILD-TYPE                                0    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           7    57
  1Q GAIN WILD-TYPE                         1    52
D2V10, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         22                14
  BLACK OR AFRICAN AMERICAN                      7                 1
  WHITE                                         57                52
[1] 4 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    2 81
  1Q GAIN WILD-TYPE  1 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   81
  1Q GAIN WILD-TYPE    1   62
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              81                62
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   12 12
  2P GAIN WILD-TYPE 79 54
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               24               133 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               12                54 
$`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-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A7PY 
       30.61        33.14         9.30        10.98         1.45         0.20 
TCGA-ED-A82E TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z TCGA-LG-A6GG 
        0.20        22.85        51.06        30.74        21.53         0.49 

$`2P GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        46.78        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-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       22.36        14.60        12.72         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-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-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-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        12.95        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73F 
        0.30        80.75        66.35        10.98         7.56        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
        0.23         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-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         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E 
        4.01         2.14        11.84        13.38         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       14.24        12.85         8.71         1.71        58.88        16.37 
TCGA-O8-A75V 
        4.44 

  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 
           25.185            13.780 
[1] "0.1 - 90.7 (25.2)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P GAIN MUTATED         7        5         0          5          1          2
  2P GAIN WILD-TYPE      58       32         2         26          4          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P GAIN MUTATED          0         0         1
  2P GAIN WILD-TYPE        1         1         1
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  7                58
  STAGE II                 5                32
  STAGE III                0                 2
  STAGE IIIA               5                26
  STAGE IIIB               1                 4
  STAGE IIIC               2                 3
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    8  7  7  2
  2P GAIN WILD-TYPE 60 34 35  6
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               8                60
  T2               7                34
  T3               7                35
  T4               2                 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"
D3V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   13  2
  2P GAIN WILD-TYPE 89  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     13    2
  2P GAIN WILD-TYPE   89    1
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              13                89
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2P GAIN MUTATED    18   1   5
  2P GAIN WILD-TYPE 102   2  32
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              18               102
  M1               1                 2
  MX               5                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   15  9
  2P GAIN WILD-TYPE 45 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15    9
  2P GAIN WILD-TYPE   45   91
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              15                45
  MALE                 9                91
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2P GAIN MUTATED                         0                       24
  2P GAIN WILD-TYPE                       2                      132
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2P GAIN MUTATED                                  0
  2P GAIN WILD-TYPE                                2
D3V8, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      24               132
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    20   4   0   0
  2P GAIN WILD-TYPE 111   7   1  12
D3V9, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              20               111
  R1               4                 7
  R2               0                 1
  RX               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     4
  2P GAIN WILD-TYPE                                1    32
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           1    19
  2P GAIN WILD-TYPE                         7    90
D3V10, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4                32
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                         19                90
[1] 4 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     1  23
  2P GAIN WILD-TYPE   2 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1   23
  2P GAIN WILD-TYPE    2  120
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              23               120
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   10 10
  2Q GAIN WILD-TYPE 81 56
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               20               137 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10                56 
$`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-ED-A7PY 
       13.64        55.69        30.61        10.98         1.45         0.20 
TCGA-ED-A82E TCGA-ES-A2HS TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z 
        0.20        22.85         1.22        51.06        30.74        21.53 
TCGA-G3-A5SM TCGA-LG-A6GG 
        4.37         0.49 

$`2Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        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-CC-5258 
        0.26        22.36         9.50        14.60        12.72         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-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-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-A1EK TCGA-DD-A39V TCGA-DD-A39Y 
       45.11        49.15         6.02        18.35        21.14         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-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F 
       80.75        66.35        10.98         9.30         7.56        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
        0.23         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U 
        0.13         0.03         0.33        60.36         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        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-A6UC 
       19.53        19.23        14.70        11.97         7.99         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       11.84        13.38         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71         1.71        58.88        16.37         4.44 

  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 
            22.19             13.84 
[1] "0.2 - 90.7 (22.2)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q GAIN MUTATED         6        6         0          3          1          1
  2Q GAIN WILD-TYPE      59       31         2         28          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q GAIN MUTATED          0         0         1
  2Q GAIN WILD-TYPE        1         1         1
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  6                59
  STAGE II                 6                31
  STAGE III                0                 2
  STAGE IIIA               3                28
  STAGE IIIB               1                 4
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    7  7  5  1
  2Q GAIN WILD-TYPE 61 34 37  7
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               7                61
  T2               7                34
  T3               5                37
  T4               1                 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"
D4V5, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   11  1
  2Q GAIN WILD-TYPE 91  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     11    1
  2Q GAIN WILD-TYPE   91    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              11                91
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2Q GAIN MUTATED    15   1   4
  2Q GAIN WILD-TYPE 105   2  33
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              15               105
  M1               1                 2
  MX               4                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   13  7
  2Q GAIN WILD-TYPE 47 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     13    7
  2Q GAIN WILD-TYPE   47   93
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              13                47
  MALE                 7                93
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2Q GAIN MUTATED                         0                       20
  2Q GAIN WILD-TYPE                       2                      136
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2Q GAIN MUTATED                                  0
  2Q GAIN WILD-TYPE                                2
D4V8, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      20               136
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    17   3   0   0
  2Q GAIN WILD-TYPE 114   8   1  12
D4V9, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              17               114
  R1               3                 8
  R2               0                 1
  RX               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     3
  2Q GAIN WILD-TYPE                                1    33
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           1    16
  2Q GAIN WILD-TYPE                         7    93
D4V10, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                33
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                         16                93
[1] 4 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     0  20
  2Q GAIN WILD-TYPE   3 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   20
  2Q GAIN WILD-TYPE    3  123
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              20               123
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    8  6
  3P GAIN WILD-TYPE 83 60
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               14               143 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                60 
$`3P GAIN MUTATED`
TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A11C TCGA-DD-A1EF 
       13.84        14.60         0.10        37.78        21.76        12.95 
TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-A73E TCGA-ES-A2HS TCGA-FV-A3R2 
       29.16         5.62        66.35         1.45        22.85         6.38 
TCGA-MI-A75G TCGA-NI-A8LF 
       14.24        16.37 

$`3P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I 
        5.03        44.42         0.26        22.36         9.50        12.72 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.10         0.13        79.73        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         2.60         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-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       49.15         6.02        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        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        10.98         9.30         7.56        10.98 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 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-A2QR 
        0.62         9.96        11.93        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         8.12         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-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         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71         1.71        58.88         4.44 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            66.35            113.00 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            14.42             13.78 
[1] "0.1 - 66.3 (14.4)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.3"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P GAIN MUTATED         8        4         0          2          0          1
  3P GAIN WILD-TYPE      57       33         2         29          5          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P GAIN MUTATED          0         0         0
  3P GAIN WILD-TYPE        1         1         2
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  8                57
  STAGE II                 4                33
  STAGE III                0                 2
  STAGE IIIA               2                29
  STAGE IIIB               0                 5
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    9  4  2  0
  3P GAIN WILD-TYPE 59 37 40  8
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               9                59
  T2               4                37
  T3               2                40
  T4               0                 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"
D5V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    6  1
  3P GAIN WILD-TYPE 96  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    1
  3P GAIN WILD-TYPE   96    2
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               6                96
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3P GAIN MUTATED    11   0   4
  3P GAIN WILD-TYPE 109   3  33
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              11               109
  M1               0                 3
  MX               4                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3 12
  3P GAIN WILD-TYPE 57 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   12
  3P GAIN WILD-TYPE   57   88
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               3                57
  MALE                12                88
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3P GAIN MUTATED                         0                       15
  3P GAIN WILD-TYPE                       2                      141
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3P GAIN MUTATED                                  0
  3P GAIN WILD-TYPE                                2
D5V8, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      15               141
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    13   0   0   2
  3P GAIN WILD-TYPE 118  11   1  10
D5V9, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              13               118
  R1               0                11
  R2               0                 1
  RX               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     2
  3P GAIN WILD-TYPE                                1    34
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           1    12
  3P GAIN WILD-TYPE                         7    97
D5V10, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                34
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                         12                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"
D5V11, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  14
  3P GAIN WILD-TYPE   3 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   14
  3P GAIN WILD-TYPE    3  129
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              14               129
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    8  8
  3Q GAIN WILD-TYPE 83 58
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16               141 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                58 
$`3Q GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A11C 
       10.13        13.84        14.60         0.10        37.78        21.76 
TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-A73E TCGA-ES-A2HS 
       12.95        29.16         5.62        66.35         1.45        22.85 
TCGA-FV-A3R2 TCGA-G3-A7M9 TCGA-MI-A75G TCGA-NI-A8LF 
        6.38         1.84        14.24        16.37 

$`3Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 
       44.42         0.26        22.36         9.50        12.72         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        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-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-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 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-A2QR TCGA-FV-A3I0 
        9.96        11.93        14.40        32.45        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         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        5.98         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
       13.38         0.49         9.57         5.10        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
        1.71        58.88         4.44 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            66.35            113.00 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            14.04             13.91 
[1] "0.1 - 66.3 (14.0)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.7"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q GAIN MUTATED         8        4         0          2          1          1
  3Q GAIN WILD-TYPE      57       33         2         29          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q GAIN MUTATED          0         0         0
  3Q GAIN WILD-TYPE        1         1         2
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  8                57
  STAGE II                 4                33
  STAGE III                0                 2
  STAGE IIIA               2                29
  STAGE IIIB               1                 4
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    9  4  4  0
  3Q GAIN WILD-TYPE 59 37 38  8
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               9                59
  T2               4                37
  T3               4                38
  T4               0                 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"
D6V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    6  1
  3Q GAIN WILD-TYPE 96  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6    1
  3Q GAIN WILD-TYPE   96    2
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               6                96
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3Q GAIN MUTATED    11   0   6
  3Q GAIN WILD-TYPE 109   3  31
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              11               109
  M1               0                 3
  MX               6                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    4 13
  3Q GAIN WILD-TYPE 56 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4   13
  3Q GAIN WILD-TYPE   56   87
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               4                56
  MALE                13                87
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3Q GAIN MUTATED                         0                       17
  3Q GAIN WILD-TYPE                       2                      139
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3Q GAIN MUTATED                                  0
  3Q GAIN WILD-TYPE                                2
D6V8, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      17               139
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    15   0   0   2
  3Q GAIN WILD-TYPE 116  11   1  10
D6V9, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              15               116
  R1               0                11
  R2               0                 1
  RX               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  0     2
  3Q GAIN WILD-TYPE                                1    34
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                           1    14
  3Q GAIN WILD-TYPE                         7    95
D6V10, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                34
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                         14                95
[1] 4 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     0  16
  3Q GAIN WILD-TYPE   3 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   16
  3Q GAIN WILD-TYPE    3  127
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              16               127
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED   11  2
  4P GAIN WILD-TYPE 80 64
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               144 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                64 
$`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-ED-A82E TCGA-ED-A8O5 TCGA-G3-A3CG 
       19.79        49.15       100.96         0.20         0.20        22.13 
TCGA-LG-A6GG 
        0.49 

$`4P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
       12.72         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-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI 
       66.31        75.65         6.71        12.95        45.11         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-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        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         1.45        27.72        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-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         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        2.14        11.84        13.38         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         8.71         1.71        58.88        16.37         4.44 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.10              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           113.00            107.11 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            2.600            14.155 
[1] "0.1 - 113.0 (2.6)"  "0.0 - 107.1 (14.2)"
[1] "hr=" "3.4"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P GAIN MUTATED         4        3         1          4          0          0
  4P GAIN WILD-TYPE      61       34         1         27          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P GAIN MUTATED          0         0         0
  4P GAIN WILD-TYPE        1         1         2
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  4                61
  STAGE II                 3                34
  STAGE III                1                 1
  STAGE IIIA               4                27
  STAGE IIIB               0                 5
  STAGE IIIC               0                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4P GAIN MUTATED    4  3  6  0
  4P GAIN WILD-TYPE 64 38 36  8
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               4                64
  T2               3                38
  T3               6                36
  T4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   11  0
  4P GAIN WILD-TYPE 91  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    0
  4P GAIN WILD-TYPE   91    3
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              11                91
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4P GAIN MUTATED    12   0   1
  4P GAIN WILD-TYPE 108   3  36
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0              12               108
  M1               0                 3
  MX               1                36
[1] 3 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    7  6
  4P GAIN WILD-TYPE 53 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      7    6
  4P GAIN WILD-TYPE   53   94
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               7                53
  MALE                 6                94
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4P GAIN MUTATED                         0                       13
  4P GAIN WILD-TYPE                       2                      143
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4P GAIN MUTATED                                  0
  4P GAIN WILD-TYPE                                2
D7V8, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      13               143
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    11   1   0   1
  4P GAIN WILD-TYPE 120  10   1  11
D7V9, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              11               120
  R1               1                10
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     5
  4P GAIN WILD-TYPE                                1    31
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1     7
  4P GAIN WILD-TYPE                         7   102
D7V10, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          5                31
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                          7               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  13
  4P GAIN WILD-TYPE   3 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   13
  4P GAIN WILD-TYPE    3  130
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              13               130
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    3  1
  4Q GAIN WILD-TYPE 88 65
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               153 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                65 
$`4Q GAIN MUTATED`
TCGA-CC-5261 TCGA-DD-A1EC TCGA-ED-A82E TCGA-G3-A3CG 
        0.39        19.79         0.20        22.13 

$`4Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-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-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
       14.60        12.72         0.07         2.86         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-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-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-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-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-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57         5.10        14.24        12.85         8.71         1.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.20              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            22.13            113.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            10.09             13.91 
[1] "0.2 - 22.1 (10.1)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.3"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q GAIN MUTATED         2        1         0          1          0          0
  4Q GAIN WILD-TYPE      63       36         2         30          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q GAIN MUTATED          0         0         0
  4Q GAIN WILD-TYPE        1         1         2
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  2                63
  STAGE II                 1                36
  STAGE III                0                 2
  STAGE IIIA               1                30
  STAGE IIIB               0                 5
  STAGE IIIC               0                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4Q GAIN MUTATED    2  1  1  0
  4Q GAIN WILD-TYPE 66 40 41  8
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               2                66
  T2               1                40
  T3               1                41
  T4               0                 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"
D8V5, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    4  0
  4Q GAIN WILD-TYPE 98  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    0
  4Q GAIN WILD-TYPE   98    3
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               4                98
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4Q GAIN MUTATED     4   0   0
  4Q GAIN WILD-TYPE 116   3  37
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               4               116
  M1               0                 3
  MX               0                37
[1] 3 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  2
  4Q GAIN WILD-TYPE 58 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    2
  4Q GAIN WILD-TYPE   58   98
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2                58
  MALE                 2                98
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4Q GAIN MUTATED                         0                        4
  4Q GAIN WILD-TYPE                       2                      152
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4Q GAIN MUTATED                                  0
  4Q GAIN WILD-TYPE                                2
D8V8, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                       4               152
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     2   1   0   1
  4Q GAIN WILD-TYPE 129  10   1  11
D8V9, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               2               129
  R1               1                10
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     2
  4Q GAIN WILD-TYPE                                1    34
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     2
  4Q GAIN WILD-TYPE                         8   107
D8V10, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                34
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          2               107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   4
  4Q GAIN WILD-TYPE   3 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    4
  4Q GAIN WILD-TYPE    3  139
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               4               139
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   33 27
  5P GAIN WILD-TYPE 58 39
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               60                97 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               27                39 
$`5P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG 
       37.32        10.13         2.99         5.03        13.84        22.36 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 
        4.24         3.32         0.10         0.13        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EE 
      113.00        51.29        90.71        79.40        66.31         6.71 
TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 
       12.95        21.14        55.69         5.62         7.66        17.59 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NK TCGA-DD-A4NO 
      102.74        13.78         0.36        73.38        39.78        73.81 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XP 
       66.35       100.96        13.41        13.35         0.23         0.20 
TCGA-ED-A82E 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-HP-A5MZ TCGA-KR-A7K2 
       58.49        22.13        14.70         4.37         2.66        11.84 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        0.49        14.24         8.71        58.88        16.37         4.44 

$`5P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       48.99        27.91        46.78        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 
       23.34         1.12        69.57        44.42         0.26         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         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 
       14.07        14.24        18.44        15.06        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       93.67        12.26         0.30        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG 
        7.56        10.98         1.45        27.72        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A12J 
       13.91         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I1 
       19.99        11.74        11.93        22.85        32.45         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        6.38         0.13         0.33         1.22        53.79        28.27 
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-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
       11.97         7.99         7.76         5.98         1.84         1.02 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
        4.01         2.14        13.38         9.57         5.10        12.85 
TCGA-MR-A8JO 
        1.71 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           113.00            107.11 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            14.04             13.91 
[1] "0.0 - 113.0 (14.0)" "0.1 - 107.1 (13.9)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P GAIN MUTATED        22       15         1         17          2          0
  5P GAIN WILD-TYPE      43       22         1         14          3          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P GAIN MUTATED          0         0         0
  5P GAIN WILD-TYPE        1         1         2
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 22                43
  STAGE II                15                22
  STAGE III                1                 1
  STAGE IIIA              17                14
  STAGE IIIB               2                 3
  STAGE IIIC               0                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED   22 17 22  1
  5P GAIN WILD-TYPE 46 24 20  7
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              22                46
  T2              17                24
  T3              22                20
  T4               1                 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"
D9V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   38  0
  5P GAIN WILD-TYPE 64  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     38    0
  5P GAIN WILD-TYPE   64    3
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              38                64
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED   49  0 13
  5P GAIN WILD-TYPE 71  3 24
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              49                71
  M1               0                 3
  MX              13                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   22 40
  5P GAIN WILD-TYPE 38 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     22   40
  5P GAIN WILD-TYPE   38   60
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              22                38
  MALE                40                60
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5P GAIN MUTATED                         0                       60
  5P GAIN WILD-TYPE                       2                       96
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5P GAIN MUTATED                                  2
  5P GAIN WILD-TYPE                                0
D9V8, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      60                96
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   51  5  0  4
  5P GAIN WILD-TYPE 80  6  1  8
D9V9, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              51                80
  R1               5                 6
  R2               0                 1
  RX               4                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0    17
  5P GAIN WILD-TYPE                                1    19
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           3    37
  5P GAIN WILD-TYPE                         5    72
D9V10, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17                19
  BLACK OR AFRICAN AMERICAN                      3                 5
  WHITE                                         37                72
[1] 4 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    1 54
  5P GAIN WILD-TYPE  2 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   54
  5P GAIN WILD-TYPE    2   89
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              54                89
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   25 21
  5Q GAIN WILD-TYPE 66 45
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               46               111 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               21                45 
$`5Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A112 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 
       37.32         2.99         5.03         0.10         0.13        83.57 
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        66.35 
TCGA-DD-A73A TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7XP TCGA-EP-A2KB 
       10.98       100.96        13.41         0.23         0.20        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
        0.62         9.96        14.40         0.03         0.39        51.06 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A5SM TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-LG-A6GG 
       30.74        22.13         4.37         2.66        11.84         0.49 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
       14.24         8.71        16.37         4.44 

$`5Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50        14.60        12.72         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-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
        0.07        79.73        37.78         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       21.76        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Z 
       49.15         6.02        29.16        18.35        13.64        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA 
       25.81        70.06        20.12       107.11        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       32.52        14.07        14.24        18.44        15.06        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73B 
       29.56        93.67        12.26         0.30        80.75         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG 
        7.56        10.98         1.45        27.72        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E 
       13.91        13.35         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HS 
        0.20        18.74        19.99        11.74        11.93        22.85 
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-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.33        60.36         1.22        53.79        28.27        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-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
       14.70        11.97         7.99         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E 
        1.02         4.01         2.14        13.38         9.57         5.10 
TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
       12.85         1.71        58.88 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           113.00            107.11 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           13.595            14.070 
[1] "0.0 - 113.0 (13.6)" "0.1 - 107.1 (14.1)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q GAIN MUTATED        20       10         1         11          2          0
  5Q GAIN WILD-TYPE      45       27         1         20          3          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q GAIN MUTATED          0         0         0
  5Q GAIN WILD-TYPE        1         1         2
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 20                45
  STAGE II                10                27
  STAGE III                1                 1
  STAGE IIIA              11                20
  STAGE IIIB               2                 3
  STAGE IIIC               0                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5Q GAIN MUTATED   20 12 15  1
  5Q GAIN WILD-TYPE 48 29 27  7
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              20                48
  T2              12                29
  T3              15                27
  T4               1                 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"
D10V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   29  0
  5Q GAIN WILD-TYPE 73  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     29    0
  5Q GAIN WILD-TYPE   73    3
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              29                73
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED   37  0 11
  5Q GAIN WILD-TYPE 83  3 26
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              37                83
  M1               0                 3
  MX              11                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   15 33
  5Q GAIN WILD-TYPE 45 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     15   33
  5Q GAIN WILD-TYPE   45   67
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              15                45
  MALE                33                67
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5Q GAIN MUTATED                         0                       47
  5Q GAIN WILD-TYPE                       2                      109
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5Q GAIN MUTATED                                  1
  5Q GAIN WILD-TYPE                                1
D10V8, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      47               109
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED   41  4  0  2
  5Q GAIN WILD-TYPE 90  7  1 10
D10V9, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              41                90
  R1               4                 7
  R2               0                 1
  RX               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0    11
  5Q GAIN WILD-TYPE                                1    25
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           3    30
  5Q GAIN WILD-TYPE                         5    79
D10V10, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                25
  BLACK OR AFRICAN AMERICAN                      3                 5
  WHITE                                         30                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"
D10V11, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  42
  5Q GAIN WILD-TYPE   2 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   42
  5Q GAIN WILD-TYPE    2  101
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              42               101
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   25 17
  6P GAIN WILD-TYPE 66 49
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               42               115 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               17                49 
$`6P GAIN MUTATED`
TCGA-BC-A10U TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-CC-5263 TCGA-CC-A3MC 
       27.52         0.26        22.36        14.60         4.24         0.13 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39X TCGA-DD-A39Y 
       37.78         7.33        45.11        49.15        55.69         5.62 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73D 
        0.36        30.61        29.56        80.75         9.30        10.98 
TCGA-DD-A73E TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A2KB 
        1.45        13.35         0.20         0.20         0.20        10.98 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25U 
        0.62        22.85        27.88         6.38         1.22        53.79 
TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A6UC 
       58.49        22.13        19.23        14.70         7.99         7.76 
TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF 
       11.84         0.49        14.24        12.85         8.71        16.37 

$`6P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       44.42        13.84         9.50        12.72         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        0.39         3.39         3.32         0.10         0.07         0.10 
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-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65         6.71        12.95         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        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-A4NA 
       17.59        20.12       102.74       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        73.81        93.67        12.26         0.30 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
       66.35        10.98         7.56        27.72       100.96        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-A7XP 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-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        32.45        19.10         8.12         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.33        60.36         0.39        51.06        28.27        30.74 
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-A5SM TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        4.37         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A8JO TCGA-NI-A4U2 
        2.14        13.38         9.57         5.10         1.71        58.88 
TCGA-O8-A75V 
        4.44 

  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 
           12.345            14.240 
[1] "0.1 - 80.8 (12.3)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P GAIN MUTATED        19       11         1          7          1          0
  6P GAIN WILD-TYPE      46       26         1         24          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P GAIN MUTATED          1         0         1
  6P GAIN WILD-TYPE        0         1         1
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 19                46
  STAGE II                11                26
  STAGE III                1                 1
  STAGE IIIA               7                24
  STAGE IIIB               1                 4
  STAGE IIIC               0                 5
  STAGE IV                 1                 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                T1 T2 T3 T4
  6P GAIN MUTATED   19 13 10  1
  6P GAIN WILD-TYPE 49 28 32  7
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              19                49
  T2              13                28
  T3              10                32
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   25  0
  6P GAIN WILD-TYPE 77  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     25    0
  6P GAIN WILD-TYPE   77    3
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              25                77
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6P GAIN MUTATED   32  2 10
  6P GAIN WILD-TYPE 88  1 27
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              32                88
  M1               2                 1
  MX              10                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   14 30
  6P GAIN WILD-TYPE 46 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     14   30
  6P GAIN WILD-TYPE   46   70
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              14                46
  MALE                30                70
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6P GAIN MUTATED                         0                       42
  6P GAIN WILD-TYPE                       2                      114
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6P GAIN MUTATED                                  2
  6P GAIN WILD-TYPE                                0
D11V8, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      42               114
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  6P GAIN MUTATED   37  3  1  3
  6P GAIN WILD-TYPE 94  8  0  9
D11V9, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              37                94
  R1               3                 8
  R2               1                 0
  RX               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0    13
  6P GAIN WILD-TYPE                                1    23
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           3    28
  6P GAIN WILD-TYPE                         5    81
D11V10, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         13                23
  BLACK OR AFRICAN AMERICAN                      3                 5
  WHITE                                         28                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"
D11V11, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     1  41
  6P GAIN WILD-TYPE   2 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   41
  6P GAIN WILD-TYPE    2  102
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              41               102
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   14  8
  6Q GAIN WILD-TYPE 77 58
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               22               135 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8                58 
$`6Q GAIN MUTATED`
TCGA-BC-A3KG TCGA-BC-A69H TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 
       22.36        14.60         4.24         0.13        37.78         7.33 
TCGA-DD-A1EH TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A73B TCGA-DD-A73D TCGA-ED-A66X 
       49.15         5.62        30.61         9.30        10.98        13.35 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SI 
       10.98         0.62        53.79        22.13        19.23        14.70 
TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H 
       11.84         0.49        14.24        12.85 

$`6Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I 
        5.03        44.42        13.84         0.26         9.50        12.72 
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-A1EG 
       66.31        19.79        75.65         6.71        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       80.75        66.35        10.98         7.56         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
      100.96        13.41        12.69        15.85        13.91         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       18.74        19.99        11.74         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       25.64         5.92        19.53        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A8JO 
        2.14        13.38         9.57         5.10         8.71         1.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.13              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            53.79            113.00 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            13.10             14.07 
[1] "0.1 - 53.8 (13.1)"  "0.0 - 113.0 (14.1)"
[1] "hr=" "1.2"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q GAIN MUTATED         9        7         1          4          0          0
  6Q GAIN WILD-TYPE      56       30         1         27          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q GAIN MUTATED          1         0         1
  6Q GAIN WILD-TYPE        0         1         1
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  9                56
  STAGE II                 7                30
  STAGE III                1                 1
  STAGE IIIA               4                27
  STAGE IIIB               0                 5
  STAGE IIIC               0                 5
  STAGE IV                 1                 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                T1 T2 T3 T4
  6Q GAIN MUTATED    9  7  6  1
  6Q GAIN WILD-TYPE 59 34 36  7
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               9                59
  T2               7                34
  T3               6                36
  T4               1                 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"
D12V5, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   15  0
  6Q GAIN WILD-TYPE 87  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     15    0
  6Q GAIN WILD-TYPE   87    3
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              15                87
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6Q GAIN MUTATED    17   2   5
  6Q GAIN WILD-TYPE 103   1  32
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              17               103
  M1               2                 1
  MX               5                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    7 17
  6Q GAIN WILD-TYPE 53 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7   17
  6Q GAIN WILD-TYPE   53   83
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               7                53
  MALE                17                83
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6Q GAIN MUTATED                         0                       23
  6Q GAIN WILD-TYPE                       2                      133
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6Q GAIN MUTATED                                  1
  6Q GAIN WILD-TYPE                                1
D12V8, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      23               133
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    19   1   1   3
  6Q GAIN WILD-TYPE 112  10   0   9
D12V9, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              19               112
  R1               1                10
  R2               1                 0
  RX               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     9
  6Q GAIN WILD-TYPE                                1    27
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           2    13
  6Q GAIN WILD-TYPE                         6    96
D12V10, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          9                27
  BLACK OR AFRICAN AMERICAN                      2                 6
  WHITE                                         13                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"
D12V11, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     1  22
  6Q GAIN WILD-TYPE   2 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   22
  6Q GAIN WILD-TYPE    2  121
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              22               121
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   29 19
  7P GAIN WILD-TYPE 62 47
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               48               109 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               19                47 
$`7P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-CC-5260 TCGA-CC-A3MB TCGA-DD-A113 
       37.32        10.13        27.52         2.86         0.10        79.73 
TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EJ 
      113.00        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        18.44        39.78        12.26        66.35        10.98 
TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-EP-A2KC 
        1.45       100.96         0.23         0.20         0.20         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        9.96        22.85         6.38         0.33        60.36         1.22 
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         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A8LF 
        4.37         7.76        11.84         0.49        14.24        16.37 

$`7P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       48.99        27.91        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-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-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-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF 
        0.46        21.76        79.40        66.31        75.65        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X 
       45.11        49.15         6.02        18.35        13.64        55.69 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81         7.66        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
        0.36        30.61        32.52        14.07        14.24        15.06 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81        93.67         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         9.30         7.56        27.72        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK 
        0.20        18.74        19.99        11.74        10.98        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 
       14.40        32.45        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-A7M7 
       25.64         5.92        19.23        14.70        11.97         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 
        1.84         1.02         2.66         4.01         2.14        13.38 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57         5.10        12.85         8.71         1.71        58.88 
TCGA-O8-A75V 
        4.44 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.10              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           113.00            107.11 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           17.405            13.640 
[1] "0.1 - 113.0 (17.4)" "0.0 - 107.1 (13.6)"
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED        19       14         0          9          2          3
  7P GAIN WILD-TYPE      46       23         2         22          3          2
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P GAIN MUTATED          0         0         0
  7P GAIN WILD-TYPE        1         1         2
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 19                46
  STAGE II                14                23
  STAGE III                0                 2
  STAGE IIIA               9                22
  STAGE IIIB               2                 3
  STAGE IIIC               3                 2
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED   20 17 12  1
  7P GAIN WILD-TYPE 48 24 30  7
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              20                48
  T2              17                24
  T3              12                30
  T4               1                 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"
D13V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   27  2
  7P GAIN WILD-TYPE 75  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     27    2
  7P GAIN WILD-TYPE   75    1
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              27                75
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED   40  0 10
  7P GAIN WILD-TYPE 80  3 27
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              40                80
  M1               0                 3
  MX              10                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   21 29
  7P GAIN WILD-TYPE 39 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     21   29
  7P GAIN WILD-TYPE   39   71
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              21                39
  MALE                29                71
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7P GAIN MUTATED                         0                       49
  7P GAIN WILD-TYPE                       2                      107
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7P GAIN MUTATED                                  1
  7P GAIN WILD-TYPE                                1
D13V8, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      49               107
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   41  5  0  3
  7P GAIN WILD-TYPE 90  6  1  9
D13V9, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              41                90
  R1               5                 6
  R2               0                 1
  RX               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     8
  7P GAIN WILD-TYPE                                0    28
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           1    38
  7P GAIN WILD-TYPE                         7    71
D13V10, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          8                28
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                         38                71
[1] 4 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    1 46
  7P GAIN WILD-TYPE  2 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1   46
  7P GAIN WILD-TYPE    2   97
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              46                97
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   29 20
  7Q GAIN WILD-TYPE 62 46
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               49               108 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               20                46 
$`7Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A3M9 
       37.32        10.13        27.52         9.50         2.86         0.10 
TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
        0.10       113.00         2.60        51.29        90.71        19.79 
TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 
        6.71        29.16        21.14         5.62        19.76        70.06 
TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73C 
       33.14        18.44        39.78        12.26        66.35         7.56 
TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S 
        1.45       100.96        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         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A4U2 
        4.37         7.76        11.84         0.49        14.24        58.88 
TCGA-NI-A8LF 
       16.37 

$`7Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       48.99        27.91        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 
        0.26        22.36        14.60        12.72         0.07         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        3.39         4.24         3.32         0.07         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       37.78        83.57        53.33         7.33         0.46        21.76 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       79.40        66.31        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 
        6.02        18.35        13.64        55.69        25.81         7.66 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       30.61        32.52        73.38        14.07        14.24        15.06 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81        93.67         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         9.30        10.98        27.72        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.91        13.35         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
        0.20        18.74        10.98        11.93        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.10        27.88         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39         1.22        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-A7M7 
       25.64         5.92        19.23        14.70        11.97         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 
        1.84         1.02         2.66         4.01         2.14        13.38 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-O8-A75V 
        9.57         5.10        12.85         8.71         1.71         4.44 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.10              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           113.00            107.11 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           14.240            13.875 
[1] "0.1 - 113.0 (14.2)" "0.0 - 107.1 (13.9)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED        18       13         0         13          1          3
  7Q GAIN WILD-TYPE      47       24         2         18          4          2
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q GAIN MUTATED          0         0         0
  7Q GAIN WILD-TYPE        1         1         2
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 18                47
  STAGE II                13                24
  STAGE III                0                 2
  STAGE IIIA              13                18
  STAGE IIIB               1                 4
  STAGE IIIC               3                 2
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED   19 16 15  1
  7Q GAIN WILD-TYPE 49 25 27  7
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              19                49
  T2              16                25
  T3              15                27
  T4               1                 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"
D14V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   29  2
  7Q GAIN WILD-TYPE 73  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     29    2
  7Q GAIN WILD-TYPE   73    1
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              29                73
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED   38  0 13
  7Q GAIN WILD-TYPE 82  3 24
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              38                82
  M1               0                 3
  MX              13                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   19 32
  7Q GAIN WILD-TYPE 41 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     19   32
  7Q GAIN WILD-TYPE   41   68
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              19                41
  MALE                32                68
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7Q GAIN MUTATED                         0                       50
  7Q GAIN WILD-TYPE                       2                      106
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7Q GAIN MUTATED                                  1
  7Q GAIN WILD-TYPE                                1
D14V8, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      50               106
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   42  4  0  3
  7Q GAIN WILD-TYPE 89  7  1  9
D14V9, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              42                89
  R1               4                 7
  R2               0                 1
  RX               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  1     9
  7Q GAIN WILD-TYPE                                0    27
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           2    38
  7Q GAIN WILD-TYPE                         6    71
D14V10, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          9                27
  BLACK OR AFRICAN AMERICAN                      2                 6
  WHITE                                         38                71
[1] 4 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    1 48
  7Q GAIN WILD-TYPE  2 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   48
  7Q GAIN WILD-TYPE    2   95
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              48                95
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   21 12
  8P GAIN WILD-TYPE 70 54
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               33               124 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                54 
$`8P GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A119 
       48.99        46.78         0.07         3.32         0.10         7.33 
TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A39X 
        2.60        90.71        19.79        12.95         6.02        55.69 
TCGA-DD-A3A1 TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-ED-A459 
        7.66        29.56        73.81        12.26        80.75        13.41 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A3JL 
       13.35         0.23         0.20         0.20        10.98         9.96 
TCGA-FV-A4ZQ TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A5SL TCGA-G3-A7M7 TCGA-KR-A7K2 
        0.39        58.49        21.53         7.99         5.98        11.84 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-MR-A8JO 
       13.38        12.85         1.71 

$`8P GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-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-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14         5.62        19.76        25.81        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        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NV 
       15.06        39.78        56.25        93.67         0.30        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
      100.96        12.69        15.85        13.91         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A8O5 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-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        1.22        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
       11.97         4.37         7.76         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        4.01         2.14         0.49         9.57         5.10        14.24 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71        58.88        16.37         4.44 

  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 
            11.84             14.78 
[1] "0.1 - 90.7 (11.8)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P GAIN MUTATED        17        6         0          9          0          0
  8P GAIN WILD-TYPE      48       31         2         22          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P GAIN MUTATED          1         0         0
  8P GAIN WILD-TYPE        0         1         2
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 17                48
  STAGE II                 6                31
  STAGE III                0                 2
  STAGE IIIA               9                22
  STAGE IIIB               0                 5
  STAGE IIIC               0                 5
  STAGE IV                 1                 0
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED   17  6 11  0
  8P GAIN WILD-TYPE 51 35 31  8
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              17                51
  T2               6                35
  T3              11                31
  T4               0                 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"
D15V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   26  0
  8P GAIN WILD-TYPE 76  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     26    0
  8P GAIN WILD-TYPE   76    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              26                76
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED   27  1  7
  8P GAIN WILD-TYPE 93  2 30
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              27                93
  M1               1                 2
  MX               7                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"
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   11 24
  8P GAIN WILD-TYPE 49 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     11   24
  8P GAIN WILD-TYPE   49   76
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              11                49
  MALE                24                76
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8P GAIN MUTATED                         1                       33
  8P GAIN WILD-TYPE                       1                      123
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8P GAIN MUTATED                                  1
  8P GAIN WILD-TYPE                                1
D15V8, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      33               123
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    27   1   1   4
  8P GAIN WILD-TYPE 104  10   0   8
D15V9, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              27               104
  R1               1                10
  R2               1                 0
  RX               4                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0    13
  8P GAIN WILD-TYPE                                1    23
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           1    20
  8P GAIN WILD-TYPE                         7    89
D15V10, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         13                23
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                         20                89
[1] 4 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     1  30
  8P GAIN WILD-TYPE   2 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   30
  8P GAIN WILD-TYPE    2  113
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              30               113
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   50 30
  8Q GAIN WILD-TYPE 41 36
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               80                77 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               30                36 
$`8Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A3KF TCGA-BC-A69H 
       48.99        46.78        27.52         2.99         0.26        14.60 
TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        0.07         3.32         0.10         0.10         0.13        79.73 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 
       53.33       113.00         7.33         2.60        21.76        90.71 
TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL 
       19.79         6.71        12.95        45.11         6.02        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 
       21.14        55.69         5.62        19.76         7.66        17.59 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN 
        0.36        73.38        14.07        18.44        15.06        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73D TCGA-DD-A73G 
       73.81        12.26         0.30        80.75        10.98       100.96 
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         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       18.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
       14.40         8.12         6.38        60.36         0.39        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ 
       28.27        30.74        58.49        21.53        22.13        19.53 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-K7-A6G5 
       14.70        11.97         7.99         5.98         2.66         4.01 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
       11.84        13.38         9.57         5.10        12.85         8.71 
TCGA-MR-A8JO TCGA-O8-A75V 
        1.71         4.44 

$`8Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        37.32        10.13        27.52        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-A5W4 TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        9.50        12.72         2.86         0.39         3.39         4.24 
TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA 
        0.07        37.78        83.57         0.46        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A3A0 
       66.31        75.65        49.15        29.16        18.35        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        14.24        39.78        56.25        93.67 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       66.35        10.98         9.30         7.56         1.45        27.72 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A8O5 
       12.69        15.85        13.91         0.20         0.20         0.20 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       19.99        11.74        32.45        19.10        27.88         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Y TCGA-G3-A3CH 
        0.03         0.33         1.22        53.79        14.86        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-GJ-A6C0 
        5.92        19.23         4.37         7.76         1.84         1.02 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A4U2 TCGA-NI-A8LF 
        2.14         0.49        14.24        58.88        16.37 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           113.00            107.11 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            12.90             16.37 
[1] "0.1 - 113.0 (12.9)" "0.0 - 107.1 (16.4)"
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED        38       20         0         16          1          1
  8Q GAIN WILD-TYPE      27       17         2         15          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q GAIN MUTATED          1         1         0
  8Q GAIN WILD-TYPE        0         0         2
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 38                27
  STAGE II                20                17
  STAGE III                0                 2
  STAGE IIIA              16                15
  STAGE IIIB               1                 4
  STAGE IIIC               1                 4
  STAGE IV                 1                 0
  STAGE IVA                1                 0
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED   39 22 19  2
  8Q GAIN WILD-TYPE 29 19 23  6
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              39                29
  T2              22                19
  T3              19                23
  T4               2                 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"
D16V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   52  1
  8Q GAIN WILD-TYPE 50  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     52    1
  8Q GAIN WILD-TYPE   50    2
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              52                50
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED   61  1 21
  8Q GAIN WILD-TYPE 59  2 16
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              61                59
  M1               1                 2
  MX              21                16
[1] 3 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   23 60
  8Q GAIN WILD-TYPE 37 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     23   60
  8Q GAIN WILD-TYPE   37   40
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              23                37
  MALE                60                40
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8Q GAIN MUTATED                         1                       81
  8Q GAIN WILD-TYPE                       1                       75
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8Q GAIN MUTATED                                  1
  8Q GAIN WILD-TYPE                                1
D16V8, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      81                75
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   67  6  1  6
  8Q GAIN WILD-TYPE 64  5  0  6
D16V9, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              67                64
  R1               6                 5
  R2               1                 0
  RX               6                 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
  8Q GAIN MUTATED                                  1    21
  8Q GAIN WILD-TYPE                                0    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           6    51
  8Q GAIN WILD-TYPE                         2    58
D16V10, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         21                15
  BLACK OR AFRICAN AMERICAN                      6                 2
  WHITE                                         51                58
[1] 4 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    2 74
  8Q GAIN WILD-TYPE  1 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2   74
  8Q GAIN WILD-TYPE    1   69
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              74                69
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    4  2
  9P GAIN WILD-TYPE 87 64
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6               151 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                64 
$`9P GAIN MUTATED`
TCGA-DD-A3A7 TCGA-DD-A4NV TCGA-ED-A66Y TCGA-EP-A2KB TCGA-G3-A25U TCGA-KR-A7K2 
       13.78        66.35         0.23        10.98        53.79        11.84 

$`9P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-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-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         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        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-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-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-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         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        4.01         2.14        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       14.24        12.85         8.71         1.71        58.88        16.37 
TCGA-O8-A75V 
        4.44 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.23              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            66.35            113.00 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            12.81             14.07 
[1] "0.2 - 66.3 (12.8)"  "0.0 - 113.0 (14.1)"
[1] "hr=" "1.3"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P GAIN MUTATED         3        0         0          3          1          0
  9P GAIN WILD-TYPE      62       37         2         28          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P GAIN MUTATED          0         0         0
  9P GAIN WILD-TYPE        1         1         2
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  3                62
  STAGE II                 0                37
  STAGE III                0                 2
  STAGE IIIA               3                28
  STAGE IIIB               1                 4
  STAGE IIIC               0                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9P GAIN MUTATED    3  0  4  0
  9P GAIN WILD-TYPE 65 41 38  8
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               3                65
  T2               0                41
  T3               4                38
  T4               0                 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"
D17V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    6  0
  9P GAIN WILD-TYPE 96  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6    0
  9P GAIN WILD-TYPE   96    3
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               6                96
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9P GAIN MUTATED     6   0   1
  9P GAIN WILD-TYPE 114   3  36
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               6               114
  M1               0                 3
  MX               1                36
[1] 3 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    3  4
  9P GAIN WILD-TYPE 57 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    4
  9P GAIN WILD-TYPE   57   96
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               3                57
  MALE                 4                96
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9P GAIN MUTATED                         0                        6
  9P GAIN WILD-TYPE                       2                      150
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9P GAIN MUTATED                                  1
  9P GAIN WILD-TYPE                                1
D17V8, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                       6               150
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED     6   0   0   1
  9P GAIN WILD-TYPE 125  11   1  11
D17V9, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0               6               125
  R1               0                11
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     3
  9P GAIN WILD-TYPE                                1    33
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           0     3
  9P GAIN WILD-TYPE                         8   106
D17V10, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                33
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          3               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"
D17V11, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0   5
  9P GAIN WILD-TYPE   3 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    5
  9P GAIN WILD-TYPE    3  138
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5               138
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    4  2
  9Q GAIN WILD-TYPE 87 64
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                6               151 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                64 
$`9Q GAIN MUTATED`
TCGA-DD-A3A6 TCGA-DD-A4NV TCGA-ED-A66Y TCGA-EP-A2KB TCGA-G3-A25U TCGA-KR-A7K2 
      107.11        66.35         0.23        10.98        53.79        11.84 

$`9Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-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-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         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-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       17.59        20.12       102.74        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        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-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-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-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         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        4.01         2.14        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       14.24        12.85         8.71         1.71        58.88        16.37 
TCGA-O8-A75V 
        4.44 

  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 
           32.815            13.910 
[1] "0.2 - 107.1 (32.8)" "0.0 - 113.0 (13.9)"
[1] "hr=" "2.6"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q GAIN MUTATED         3        1         0          3          0          0
  9Q GAIN WILD-TYPE      62       36         2         28          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q GAIN MUTATED          0         0         0
  9Q GAIN WILD-TYPE        1         1         2
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  3                62
  STAGE II                 1                36
  STAGE III                0                 2
  STAGE IIIA               3                28
  STAGE IIIB               0                 5
  STAGE IIIC               0                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    3  1  3  0
  9Q GAIN WILD-TYPE 65 40 39  8
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               3                65
  T2               1                40
  T3               3                39
  T4               0                 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"
D18V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    6  0
  9Q GAIN WILD-TYPE 96  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      6    0
  9Q GAIN WILD-TYPE   96    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               6                96
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9Q GAIN MUTATED     6   0   1
  9Q GAIN WILD-TYPE 114   3  36
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               6               114
  M1               0                 3
  MX               1                36
[1] 3 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    4  3
  9Q GAIN WILD-TYPE 56 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    3
  9Q GAIN WILD-TYPE   56   97
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               4                56
  MALE                 3                97
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9Q GAIN MUTATED                         0                        6
  9Q GAIN WILD-TYPE                       2                      150
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9Q GAIN MUTATED                                  1
  9Q GAIN WILD-TYPE                                1
D18V8, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                       6               150
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED     6   0   0   1
  9Q GAIN WILD-TYPE 125  11   1  11
D18V9, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               6               125
  R1               0                11
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     3
  9Q GAIN WILD-TYPE                                1    33
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           0     4
  9Q GAIN WILD-TYPE                         8   105
D18V10, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                33
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          4               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"
D18V11, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0   6
  9Q GAIN WILD-TYPE   3 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    6
  9Q GAIN WILD-TYPE    3  137
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               6               137
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED   15  7
  10P GAIN WILD-TYPE 76 59
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                135 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 7                 59 
$`10P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A1EL 
       37.32        10.13         0.10        79.73        37.78        13.64 
TCGA-DD-A3A9 TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66X 
       30.61        66.35        10.98       100.96        13.41        13.35 
TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A5SJ 
        0.23         0.20        10.98        22.85         0.39        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-MR-A8JO TCGA-NI-A8LF 
        7.99         4.37         1.71        16.37 

$`10P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.07         0.13        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-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        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-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-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
        1.45        27.72        12.69        15.85        13.91         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 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-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       11.74         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33        60.36         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-A6UC TCGA-G3-A7M7 
        5.92        19.53        19.23        14.70         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  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 
             12.66              14.24 
[1] "0.1 - 101.0 (12.7)" "0.0 - 113.0 (14.2)"
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10P GAIN MUTATED         7        6         0          7          0
  10P GAIN WILD-TYPE      58       31         2         24          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P GAIN MUTATED            0        0         0         1
  10P GAIN WILD-TYPE          5        1         1         1
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   7                 58
  STAGE II                  6                 31
  STAGE III                 0                  2
  STAGE IIIA                7                 24
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10P GAIN MUTATED    7  7  8  1
  10P GAIN WILD-TYPE 61 34 34  7
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                7                 61
  T2                7                 34
  T3                8                 34
  T4                1                  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"
D19V5, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   12  0
  10P GAIN WILD-TYPE 90  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12    0
  10P GAIN WILD-TYPE   90    3
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               12                 90
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10P GAIN MUTATED    15   1   7
  10P GAIN WILD-TYPE 105   2  30
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0               15                105
  M1                1                  2
  MX                7                 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"
D19V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    9 14
  10P GAIN WILD-TYPE 51 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9   14
  10P GAIN WILD-TYPE   51   86
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                9                 51
  MALE                 14                 86
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10P GAIN MUTATED                         1                       22
  10P GAIN WILD-TYPE                       1                      134
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10P GAIN MUTATED                                  0
  10P GAIN WILD-TYPE                                2
D19V8, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       22                134
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    20   1   0   2
  10P GAIN WILD-TYPE 111  10   1  10
D19V9, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               20                111
  R1                1                 10
  R2                0                  1
  RX                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     6
  10P GAIN WILD-TYPE                                1    30
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           2    15
  10P GAIN WILD-TYPE                         6    94
D19V10, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 30
  BLACK OR AFRICAN AMERICAN                       2                  6
  WHITE                                          15                 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"
D19V11, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  22
  10P GAIN WILD-TYPE   3 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   22
  10P GAIN WILD-TYPE    3  121
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               22                121
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    9  4
  10Q GAIN WILD-TYPE 82 62
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                144 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 62 
$`10Q GAIN MUTATED`
TCGA-DD-A113 TCGA-DD-A39Z TCGA-DD-A3A9 TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A66X 
       79.73        19.76        30.61        66.35       100.96        13.35 
TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A5SL TCGA-G3-A5SM 
        0.20        10.98        22.85         0.39         7.99         4.37 
TCGA-NI-A8LF 
       16.37 

$`10Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-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-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         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-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-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-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-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-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       27.72        13.41        12.69        15.85        13.91         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         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-A2HT 
       19.99        11.74         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-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-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71         1.71        58.88         4.44 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.20               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            100.96             113.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            16.370             13.875 
[1] "0.2 - 101.0 (16.4)" "0.0 - 113.0 (13.9)"
[1] "hr=" "1.6"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q GAIN MUTATED         5        3         0          4          0
  10Q GAIN WILD-TYPE      60       34         2         27          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q GAIN MUTATED            0        0         0         1
  10Q GAIN WILD-TYPE          5        1         1         1
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   5                 60
  STAGE II                  3                 34
  STAGE III                 0                  2
  STAGE IIIA                4                 27
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10Q GAIN MUTATED    5  3  4  1
  10Q GAIN WILD-TYPE 63 38 38  7
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                5                 63
  T2                3                 38
  T3                4                 38
  T4                1                  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"
D20V5, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    6  0
  10Q GAIN WILD-TYPE 96  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    0
  10Q GAIN WILD-TYPE   96    3
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                6                 96
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10Q GAIN MUTATED     9   1   3
  10Q GAIN WILD-TYPE 111   2  34
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                9                111
  M1                1                  2
  MX                3                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    6  7
  10Q GAIN WILD-TYPE 54 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    7
  10Q GAIN WILD-TYPE   54   93
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                6                 54
  MALE                  7                 93
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10Q GAIN MUTATED                         0                       13
  10Q GAIN WILD-TYPE                       2                      143
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10Q GAIN MUTATED                                  0
  10Q GAIN WILD-TYPE                                2
D20V8, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       13                143
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    13   0   0   0
  10Q GAIN WILD-TYPE 118  11   1  12
D20V9, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               13                118
  R1                0                 11
  R2                0                  1
  RX                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     2
  10Q GAIN WILD-TYPE                                1    34
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           0    10
  10Q GAIN WILD-TYPE                         8    99
D20V10, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                 34
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                          10                 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"
D20V11, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0  12
  10Q GAIN WILD-TYPE   3 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   12
  10Q GAIN WILD-TYPE    3  131
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               12                131
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    8  2
  11P GAIN WILD-TYPE 83 64
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                147 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 64 
$`11P GAIN MUTATED`
TCGA-BC-A69H TCGA-CC-A3M9 TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A4NV TCGA-ED-A66Y 
       14.60         0.10         7.33         5.62        66.35         0.23 
TCGA-ED-A82E TCGA-FV-A4ZQ TCGA-G3-A3CG TCGA-LG-A6GG 
        0.20         0.39        22.13         0.49 

$`11P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.84         0.26        22.36         9.50 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       12.72         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-A114 
        3.32         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-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-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        6.38         0.13         0.03         0.33        60.36         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        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         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57         5.10        14.24        12.85         8.71         1.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.10               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             66.35             113.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             3.055             14.240 
[1] "0.1 - 66.3 (3.1)"   "0.0 - 113.0 (14.2)"
[1] "hr=" "1"  
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P GAIN MUTATED         4        2         0          4          0
  11P GAIN WILD-TYPE      61       35         2         27          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P GAIN MUTATED            0        1         0         0
  11P GAIN WILD-TYPE          5        0         1         2
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   4                 61
  STAGE II                  2                 35
  STAGE III                 0                  2
  STAGE IIIA                4                 27
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  1                  0
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    4  2  5  0
  11P GAIN WILD-TYPE 64 39 37  8
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                4                 64
  T2                2                 39
  T3                5                 37
  T4                0                  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"
D21V5, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    6  0
  11P GAIN WILD-TYPE 96  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6    0
  11P GAIN WILD-TYPE   96    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                6                 96
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11P GAIN MUTATED     9   1   1
  11P GAIN WILD-TYPE 111   2  36
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                9                111
  M1                1                  2
  MX                1                 36
[1] 3 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    3  8
  11P GAIN WILD-TYPE 57 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    8
  11P GAIN WILD-TYPE   57   92
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                3                 57
  MALE                  8                 92
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11P GAIN MUTATED                         0                       11
  11P GAIN WILD-TYPE                       2                      145
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11P GAIN MUTATED                                  0
  11P GAIN WILD-TYPE                                2
D21V8, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       11                145
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED     8   1   1   1
  11P GAIN WILD-TYPE 123  10   0  11
D21V9, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                8                123
  R1                1                 10
  R2                1                  0
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     5
  11P GAIN WILD-TYPE                                1    31
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           0     6
  11P GAIN WILD-TYPE                         8   103
D21V10, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 31
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                           6                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  11
  11P GAIN WILD-TYPE   3 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   11
  11P GAIN WILD-TYPE    3  132
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               11                132
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    7  3
  11Q GAIN WILD-TYPE 84 63
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                147 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 63 
$`11Q GAIN MUTATED`
TCGA-BC-A69I TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NV TCGA-ED-A66Y 
       12.72         7.33         5.62        25.81        66.35         0.23 
TCGA-ED-A82E TCGA-FV-A4ZQ TCGA-G3-A3CG TCGA-LG-A6GG 
        0.20         0.39        22.13         0.49 

$`11Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-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-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       14.60         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-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-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-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 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        6.38         0.13         0.03         0.33        60.36         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        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         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57         5.10        14.24        12.85         8.71         1.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.20               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             66.35             113.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             6.475             14.240 
[1] "0.2 - 66.3 (6.5)"   "0.0 - 113.0 (14.2)"
[1] "hr=" "1.2"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED         6        1         0          3          0
  11Q GAIN WILD-TYPE      59       36         2         28          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q GAIN MUTATED            0        1         0         0
  11Q GAIN WILD-TYPE          5        0         1         2
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   6                 59
  STAGE II                  1                 36
  STAGE III                 0                  2
  STAGE IIIA                3                 28
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  1                  0
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN MUTATED    6  1  4  0
  11Q GAIN WILD-TYPE 62 40 38  8
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                6                 62
  T2                1                 40
  T3                4                 38
  T4                0                  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"
D22V5, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    6  0
  11Q GAIN WILD-TYPE 96  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    0
  11Q GAIN WILD-TYPE   96    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                6                 96
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11Q GAIN MUTATED     9   1   1
  11Q GAIN WILD-TYPE 111   2  36
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                9                111
  M1                1                  2
  MX                1                 36
[1] 3 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    3  8
  11Q GAIN WILD-TYPE 57 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    8
  11Q GAIN WILD-TYPE   57   92
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 57
  MALE                  8                 92
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11Q GAIN MUTATED                         0                       11
  11Q GAIN WILD-TYPE                       2                      145
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11Q GAIN MUTATED                                  0
  11Q GAIN WILD-TYPE                                2
D22V8, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       11                145
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED     8   1   1   1
  11Q GAIN WILD-TYPE 123  10   0  11
D22V9, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                8                123
  R1                1                 10
  R2                1                  0
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     4
  11Q GAIN WILD-TYPE                                1    32
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           0     7
  11Q GAIN WILD-TYPE                         8   102
D22V10, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                 32
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                           7                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  10
  11Q GAIN WILD-TYPE   3 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   10
  11Q GAIN WILD-TYPE    3  133
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               10                133
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   12  4
  12P GAIN WILD-TYPE 79 62
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                16                141 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                 62 
$`12P GAIN MUTATED`
TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A3A7 TCGA-DD-A4NR TCGA-DD-A73G TCGA-ED-A66Y 
        2.60        12.95        13.78         0.30       100.96         0.23 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A3JL TCGA-FV-A3I0 TCGA-G3-A25T 
        0.20         0.20         0.20         9.96        27.88        51.06 
TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-MI-A75C TCGA-NI-A8LF 
        1.84        11.84         9.57        16.37 

$`12P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-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-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         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        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS 
       56.25        29.56        73.81        93.67        12.26        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       27.72        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 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-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10         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-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        7.76         5.98         1.02         2.66         4.01         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       13.38         0.49         5.10        14.24        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
        1.71        58.88         4.44 

  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 
             9.765             14.400 
[1] "0.2 - 101.0 (9.8)"  "0.0 - 113.0 (14.4)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P GAIN MUTATED         8        3         0          4          2
  12P GAIN WILD-TYPE      57       34         2         27          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P GAIN MUTATED            0        0         0         0
  12P GAIN WILD-TYPE          5        1         1         2
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   8                 57
  STAGE II                  3                 34
  STAGE III                 0                  2
  STAGE IIIA                4                 27
  STAGE IIIB                2                  3
  STAGE IIIC                0                  5
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    8  3  6  0
  12P GAIN WILD-TYPE 60 38 36  8
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                8                 60
  T2                3                 38
  T3                6                 36
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   11  0
  12P GAIN WILD-TYPE 91  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     11    0
  12P GAIN WILD-TYPE   91    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               11                 91
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12P GAIN MUTATED    14   0   3
  12P GAIN WILD-TYPE 106   3  34
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               14                106
  M1                0                  3
  MX                3                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    8  9
  12P GAIN WILD-TYPE 52 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8    9
  12P GAIN WILD-TYPE   52   91
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                8                 52
  MALE                  9                 91
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12P GAIN MUTATED                         0                       15
  12P GAIN WILD-TYPE                       2                      141
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12P GAIN MUTATED                                  2
  12P GAIN WILD-TYPE                                0
D23V8, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       15                141
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    15   0   0   1
  12P GAIN WILD-TYPE 116  11   1  11
D23V9, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               15                116
  R1                0                 11
  R2                0                  1
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     5
  12P GAIN WILD-TYPE                                1    31
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           1    10
  12P GAIN WILD-TYPE                         7    99
D23V10, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 31
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                          10                 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"
D23V11, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  15
  12P GAIN WILD-TYPE   3 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   15
  12P GAIN WILD-TYPE    3  128
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               15                128
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   15  5
  12Q GAIN WILD-TYPE 76 61
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                20                137 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 61 
$`12Q GAIN MUTATED`
TCGA-BC-A3KF TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A3A7 TCGA-DD-A4ND 
        0.26         2.60        12.95        29.16        13.78        73.38 
TCGA-DD-A4NH TCGA-DD-A4NR TCGA-DD-A73G TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ 
       14.24         0.30       100.96         0.23         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A3JL TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A7M9 TCGA-KR-A7K2 
        0.20         9.96        27.88        51.06         1.84        11.84 
TCGA-MI-A75C TCGA-NI-A8LF 
        9.57        16.37 

$`12Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        44.42        13.84        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       12.72         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        14.07        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         1.45        27.72        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
       13.91        13.35         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        11.74        10.98         0.62        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.10         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.03         0.33        60.36         0.39         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-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-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.99         4.37         7.76         5.98         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G 
        4.01         2.14        13.38         0.49         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71         1.71        58.88         4.44 

  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 
              10.9               14.4 
[1] "0.2 - 101.0 (10.9)" "0.0 - 113.0 (14.4)"
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q GAIN MUTATED        10        3         0          4          3
  12Q GAIN WILD-TYPE      55       34         2         27          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q GAIN MUTATED            1        0         0         0
  12Q GAIN WILD-TYPE          4        1         1         2
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  10                 55
  STAGE II                  3                 34
  STAGE III                 0                  2
  STAGE IIIA                4                 27
  STAGE IIIB                3                  2
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN MUTATED   11  3  7  0
  12Q GAIN WILD-TYPE 57 38 35  8
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               11                 57
  T2                3                 38
  T3                7                 35
  T4                0                  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"
D24V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   13  1
  12Q GAIN WILD-TYPE 89  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     13    1
  12Q GAIN WILD-TYPE   89    2
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               13                 89
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12Q GAIN MUTATED    18   0   3
  12Q GAIN WILD-TYPE 102   3  34
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               18                102
  M1                0                  3
  MX                3                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   12  9
  12Q GAIN WILD-TYPE 48 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12    9
  12Q GAIN WILD-TYPE   48   91
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               12                 48
  MALE                  9                 91
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12Q GAIN MUTATED                         0                       19
  12Q GAIN WILD-TYPE                       2                      137
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12Q GAIN MUTATED                                  2
  12Q GAIN WILD-TYPE                                0
D24V8, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       19                137
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    19   0   0   1
  12Q GAIN WILD-TYPE 112  11   1  11
D24V9, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               19                112
  R1                0                 11
  R2                0                  1
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     5
  12Q GAIN WILD-TYPE                                1    31
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           1    14
  12Q GAIN WILD-TYPE                         7    95
D24V10, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 31
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                          14                 95
[1] 4 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  18
  12Q GAIN WILD-TYPE   3 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   18
  12Q GAIN WILD-TYPE    3  125
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               18                125
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    3  5
  13Q GAIN WILD-TYPE 88 61
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                149 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 61 
$`13Q GAIN MUTATED`
TCGA-BC-A3KF TCGA-CC-5263 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A3A7 TCGA-ED-A66Y 
        0.26         4.24        45.11        29.16        13.78         0.23 
TCGA-EP-A3JL TCGA-FV-A23B 
        9.96        32.45 

$`13Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        44.42        13.84        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
       12.72         0.07         2.86         0.39         3.39         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-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-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-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        11.74        10.98         0.62        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       22.85        14.40        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-A7M7 
       14.70        11.97         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71         1.71        58.88        16.37         4.44 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.23               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             45.11             113.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             11.87              14.07 
[1] "0.2 - 45.1 (11.9)"  "0.0 - 113.0 (14.1)"
[1] "hr=" "2.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q GAIN MUTATED         3        1         0          2          1
  13Q GAIN WILD-TYPE      62       36         2         29          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q GAIN MUTATED            1        0         0         0
  13Q GAIN WILD-TYPE          4        1         1         2
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   3                 62
  STAGE II                  1                 36
  STAGE III                 0                  2
  STAGE IIIA                2                 29
  STAGE IIIB                1                  4
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    4  1  3  0
  13Q GAIN WILD-TYPE 64 40 39  8
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                4                 64
  T2                1                 40
  T3                3                 39
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    5  1
  13Q GAIN WILD-TYPE 97  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5    1
  13Q GAIN WILD-TYPE   97    2
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                5                 97
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  13Q GAIN MUTATED     7   0   1
  13Q GAIN WILD-TYPE 113   3  36
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                7                113
  M1                0                  3
  MX                1                 36
[1] 3 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    4  4
  13Q GAIN WILD-TYPE 56 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    4
  13Q GAIN WILD-TYPE   56   96
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                 56
  MALE                  4                 96
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  13Q GAIN MUTATED                         0                        8
  13Q GAIN WILD-TYPE                       2                      148
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  13Q GAIN MUTATED                                  0
  13Q GAIN WILD-TYPE                                2
D25V8, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                        8                148
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED     6   0   0   1
  13Q GAIN WILD-TYPE 125  11   1  11
D25V9, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                6                125
  R1                0                 11
  R2                0                  1
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     2
  13Q GAIN WILD-TYPE                                1    34
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           0     5
  13Q GAIN WILD-TYPE                         8   104
D25V10, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                 34
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                           5                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"
D25V11, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   6
  13Q GAIN WILD-TYPE   3 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    6
  13Q GAIN WILD-TYPE    3  137
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                6                137
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    6  3
  14Q GAIN WILD-TYPE 85 63
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                148 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 63 
$`14Q GAIN MUTATED`
TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A4ND TCGA-ED-A66Y TCGA-ES-A2HS 
        0.10        37.78         7.33        73.38         0.23        22.85 
TCGA-FV-A3I0 TCGA-G3-A3CG TCGA-KR-A7K2 
       27.88        22.13        11.84 

$`14Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-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-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         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-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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 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-A2QR TCGA-FV-A3I1 
        9.96        11.93        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-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-A7M7 
       14.70        11.97         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 
        1.84         1.02         2.66         4.01         2.14        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        1.71        58.88        16.37         4.44 

  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 
            22.130             13.875 
[1] "0.1 - 73.4 (22.1)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.2"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q GAIN MUTATED         4        2         0          2          0
  14Q GAIN WILD-TYPE      61       35         2         29          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q GAIN MUTATED            0        1         0         0
  14Q GAIN WILD-TYPE          5        0         1         2
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   4                 61
  STAGE II                  2                 35
  STAGE III                 0                  2
  STAGE IIIA                2                 29
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  1                  0
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  14Q GAIN MUTATED    4  2  3  0
  14Q GAIN WILD-TYPE 64 39 39  8
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                4                 64
  T2                2                 39
  T3                3                 39
  T4                0                  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"
D26V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    6  0
  14Q GAIN WILD-TYPE 96  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      6    0
  14Q GAIN WILD-TYPE   96    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                6                 96
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  14Q GAIN MUTATED     7   1   1
  14Q GAIN WILD-TYPE 113   2  36
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                7                113
  M1                1                  2
  MX                1                 36
[1] 3 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    3  6
  14Q GAIN WILD-TYPE 57 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3    6
  14Q GAIN WILD-TYPE   57   94
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                3                 57
  MALE                  6                 94
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  14Q GAIN MUTATED                         0                        7
  14Q GAIN WILD-TYPE                       2                      149
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  14Q GAIN MUTATED                                  2
  14Q GAIN WILD-TYPE                                0
D26V8, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                        7                149
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED     7   1   1   0
  14Q GAIN WILD-TYPE 124  10   0  12
D26V9, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                7                124
  R1                1                 10
  R2                1                  0
  RX                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     3
  14Q GAIN WILD-TYPE                                1    33
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           1     5
  14Q GAIN WILD-TYPE                         7   104
D26V10, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                 33
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                           5                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"
D26V11, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0   8
  14Q GAIN WILD-TYPE   3 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    8
  14Q GAIN WILD-TYPE    3  135
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                8                135
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   12  3
  15Q GAIN WILD-TYPE 79 63
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                142 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 63 
$`15Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10Y TCGA-BC-A3KG TCGA-CC-A3M9 TCGA-DD-A4NI TCGA-DD-A4NV 
       37.32        23.34        22.36         0.10        18.44        66.35 
TCGA-DD-A73G TCGA-ED-A66X TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X 
      100.96        13.35        22.85         0.39        51.06        58.49 
TCGA-G3-A6UC TCGA-MI-A75G TCGA-MR-A8JO 
        7.76        14.24         1.71 

$`15Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       13.84         0.26         9.50        14.60        12.72         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-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-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.07        14.24        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       73.81        93.67        12.26         0.30        80.75        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 
        9.30         7.56        10.98         1.45        27.72        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       12.69        15.85        13.91         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-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-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       11.84        13.38         0.49         9.57         5.10        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71        58.88        16.37         4.44 

  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 
             22.36              13.71 
[1] "0.1 - 101.0 (22.4)" "0.0 - 113.0 (13.7)"
[1] "hr=" "2.6"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  15Q GAIN MUTATED         4        4         0          4          1
  15Q GAIN WILD-TYPE      61       33         2         27          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q GAIN MUTATED            0        0         0         0
  15Q GAIN WILD-TYPE          5        1         1         2
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   4                 61
  STAGE II                  4                 33
  STAGE III                 0                  2
  STAGE IIIA                4                 27
  STAGE IIIB                1                  4
  STAGE IIIC                0                  5
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  15Q GAIN MUTATED    4  5  5  1
  15Q GAIN WILD-TYPE 64 36 37  7
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                4                 64
  T2                5                 36
  T3                5                 37
  T4                1                  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"
D27V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   10  0
  15Q GAIN WILD-TYPE 92  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     10    0
  15Q GAIN WILD-TYPE   92    3
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               10                 92
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  15Q GAIN MUTATED    11   0   4
  15Q GAIN WILD-TYPE 109   3  33
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               11                109
  M1                0                  3
  MX                4                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    4 11
  15Q GAIN WILD-TYPE 56 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4   11
  15Q GAIN WILD-TYPE   56   89
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                4                 56
  MALE                 11                 89
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  15Q GAIN MUTATED                         1                       14
  15Q GAIN WILD-TYPE                       1                      142
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  15Q GAIN MUTATED                                  0
  15Q GAIN WILD-TYPE                                2
D27V8, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       14                142
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    13   1   0   1
  15Q GAIN WILD-TYPE 118  10   1  11
D27V9, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               13                118
  R1                1                 10
  R2                0                  1
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     3
  15Q GAIN WILD-TYPE                                1    33
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           0    12
  15Q GAIN WILD-TYPE                         8    97
D27V10, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                 33
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                          12                 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"
D27V11, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  14
  15Q GAIN WILD-TYPE   3 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   14
  15Q GAIN WILD-TYPE    3  129
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               14                129
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   10  5
  16P GAIN WILD-TYPE 81 61
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                142 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 61 
$`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-ED-A459 TCGA-ED-A7PZ TCGA-ED-A82E TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SM 
       13.41         0.20         0.20         1.22        51.06         4.37 
TCGA-KR-A7K2 TCGA-MR-A8JO TCGA-NI-A8LF 
       11.84         1.71        16.37 

$`16P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-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-A114 TCGA-DD-A115 
        0.10         0.07         0.10         0.13        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-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-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       70.06        17.59        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        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-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-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-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         7.99 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        2.14        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71        58.88         4.44 

  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 
             10.13              14.32 
[1] "0.2 - 102.7 (10.1)" "0.0 - 113.0 (14.3)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED         5        5         1          2          0
  16P GAIN WILD-TYPE      60       32         1         29          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P GAIN MUTATED            0        0         0         0
  16P GAIN WILD-TYPE          5        1         1         2
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   5                 60
  STAGE II                  5                 32
  STAGE III                 1                  1
  STAGE IIIA                2                 29
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    5  5  5  0
  16P GAIN WILD-TYPE 63 36 37  8
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                5                 63
  T2                5                 36
  T3                5                 37
  T4                0                  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"
D28V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   10  0
  16P GAIN WILD-TYPE 92  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     10    0
  16P GAIN WILD-TYPE   92    3
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               10                 92
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16P GAIN MUTATED    11   0   4
  16P GAIN WILD-TYPE 109   3  33
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               11                109
  M1                0                  3
  MX                4                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    5 10
  16P GAIN WILD-TYPE 55 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5   10
  16P GAIN WILD-TYPE   55   90
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                5                 55
  MALE                 10                 90
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16P GAIN MUTATED                         1                       13
  16P GAIN WILD-TYPE                       1                      143
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16P GAIN MUTATED                                  1
  16P GAIN WILD-TYPE                                1
D28V8, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       13                143
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    13   1   0   1
  16P GAIN WILD-TYPE 118  10   1  11
D28V9, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               13                118
  R1                1                 10
  R2                0                  1
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     3
  16P GAIN WILD-TYPE                                1    33
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           2    10
  16P GAIN WILD-TYPE                         6    99
D28V10, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                 33
  BLACK OR AFRICAN AMERICAN                       2                  6
  WHITE                                          10                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  13
  16P GAIN WILD-TYPE   3 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   13
  16P GAIN WILD-TYPE    3  130
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               13                130
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    5  2
  16Q GAIN WILD-TYPE 86 64
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                150 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 64 
$`16Q GAIN MUTATED`
TCGA-BC-A10R TCGA-DD-A1EL TCGA-ED-A82E TCGA-G3-A25T TCGA-G3-A5SM TCGA-KR-A7K2 
       10.13        13.64         0.20        51.06         4.37        11.84 
TCGA-MR-A8JO 
        1.71 

$`16Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       12.72         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-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-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        29.16        18.35        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.03         0.33        60.36         0.39         1.22        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-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.99         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        4.01         2.14        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       14.24        12.85         8.71        58.88        16.37         4.44 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.20               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             51.06             113.00 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             10.13              14.24 
[1] "0.2 - 51.1 (10.1)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED         2        2         0          2          0
  16Q GAIN WILD-TYPE      63       35         2         29          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q GAIN MUTATED            0        0         0         0
  16Q GAIN WILD-TYPE          5        1         1         2
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   2                 63
  STAGE II                  2                 35
  STAGE III                 0                  2
  STAGE IIIA                2                 29
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    2  2  3  0
  16Q GAIN WILD-TYPE 66 39 39  8
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                2                 66
  T2                2                 39
  T3                3                 39
  T4                0                  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"
D29V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    5  0
  16Q GAIN WILD-TYPE 97  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5    0
  16Q GAIN WILD-TYPE   97    3
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                5                 97
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16Q GAIN MUTATED     5   0   2
  16Q GAIN WILD-TYPE 115   3  35
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                5                115
  M1                0                  3
  MX                2                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  4
  16Q GAIN WILD-TYPE 57 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    4
  16Q GAIN WILD-TYPE   57   96
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 57
  MALE                  4                 96
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16Q GAIN MUTATED                         1                        5
  16Q GAIN WILD-TYPE                       1                      151
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16Q GAIN MUTATED                                  1
  16Q GAIN WILD-TYPE                                1
D29V8, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                        5                151
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED     6   0   0   1
  16Q GAIN WILD-TYPE 125  11   1  11
D29V9, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                6                125
  R1                0                 11
  R2                0                  1
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     1
  16Q GAIN WILD-TYPE                                1    35
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           1     5
  16Q GAIN WILD-TYPE                         7   104
D29V10, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 35
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                           5                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"
D29V11, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0   5
  16Q GAIN WILD-TYPE   3 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    5
  16Q GAIN WILD-TYPE    3  138
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                138
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    9  5
  17P GAIN WILD-TYPE 82 61
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                14                143 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 61 
$`17P GAIN MUTATED`
TCGA-BC-A10Q TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A3A7 TCGA-DD-A4NO TCGA-DD-A4NP 
       37.32         0.10        37.78        13.78        73.81        93.67 
TCGA-DD-A73D TCGA-ED-A66X TCGA-ED-A66Y TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZP 
       10.98        13.35         0.23        10.98        22.85        60.36 
TCGA-G3-A25W TCGA-NI-A8LF 
       30.74        16.37 

$`17P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       12.72         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-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-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 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       29.56        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        9.30         7.56         1.45        27.72       100.96        13.41 
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-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         9.96        11.93        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.39         1.22        51.06        53.79        28.27        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         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71         1.71        58.88         4.44 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.10               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             93.67             113.00 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             19.61              13.84 
[1] "0.1 - 93.7 (19.6)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.5"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P GAIN MUTATED         5        2         0          4          2
  17P GAIN WILD-TYPE      60       35         2         27          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P GAIN MUTATED            0        0         0         0
  17P GAIN WILD-TYPE          5        1         1         2
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   5                 60
  STAGE II                  2                 35
  STAGE III                 0                  2
  STAGE IIIA                4                 27
  STAGE IIIB                2                  3
  STAGE IIIC                0                  5
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17P GAIN MUTATED    5  3  6  0
  17P GAIN WILD-TYPE 63 38 36  8
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                5                 63
  T2                3                 38
  T3                6                 36
  T4                0                  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"
D30V5, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    7  0
  17P GAIN WILD-TYPE 95  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      7    0
  17P GAIN WILD-TYPE   95    3
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                7                 95
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17P GAIN MUTATED     9   0   5
  17P GAIN WILD-TYPE 111   3  32
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                9                111
  M1                0                  3
  MX                5                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    5  9
  17P GAIN WILD-TYPE 55 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    9
  17P GAIN WILD-TYPE   55   91
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                5                 55
  MALE                  9                 91
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17P GAIN MUTATED                         0                       14
  17P GAIN WILD-TYPE                       2                      142
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17P GAIN MUTATED                                  0
  17P GAIN WILD-TYPE                                2
D30V8, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       14                142
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    12   2   0   0
  17P GAIN WILD-TYPE 119   9   1  12
D30V9, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               12                119
  R1                2                  9
  R2                0                  1
  RX                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     3
  17P GAIN WILD-TYPE                                1    33
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           1     9
  17P GAIN WILD-TYPE                         7   100
D30V10, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                 33
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                           9                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  13
  17P GAIN WILD-TYPE   3 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   13
  17P GAIN WILD-TYPE    3  130
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               13                130
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   22 18
  17Q GAIN WILD-TYPE 69 48
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                40                117 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                 48 
$`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-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MC 
       13.84        14.60         2.86         0.39         4.24         0.13 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EI TCGA-DD-A39Y 
       37.78         7.33         2.60        79.40         6.02         5.62 
TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73D 
       17.59        13.78        30.61        73.81        93.67        10.98 
TCGA-DD-A73E TCGA-ED-A66X TCGA-ED-A66Y TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
        1.45        13.35         0.23        10.98         0.62        22.85 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CK 
        0.03        60.36        53.79        30.74        21.53        19.23 
TCGA-G3-A5SJ TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
       11.97         8.71        16.37         4.44 

$`17Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       27.91        10.13        46.78        27.52        27.52        25.32 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I 
       69.57        44.42         0.26        22.36         9.50        12.72 
TCGA-CC-5258 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        0.07         3.39         3.32         0.10         0.07         0.10 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
       79.73        83.57        53.33       113.00         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        90.71        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11        49.15        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-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        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        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
       10.98         9.30         7.56        27.72       100.96        13.41 
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-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        9.96        11.93        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
        8.12         6.38         0.13         0.33         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
       51.06        28.27        58.49        14.86        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
        5.92        19.53        14.70         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
       12.85         1.71        58.88 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.03               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             93.67             113.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             12.66              14.24 
[1] "0.0 - 93.7 (12.7)"  "0.1 - 113.0 (14.2)"
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED        18        7         0          7          2
  17Q GAIN WILD-TYPE      47       30         2         24          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q GAIN MUTATED            1        1         0         1
  17Q GAIN WILD-TYPE          4        0         1         1
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  18                 47
  STAGE II                  7                 30
  STAGE III                 0                  2
  STAGE IIIA                7                 24
  STAGE IIIB                2                  3
  STAGE IIIC                1                  4
  STAGE IV                  1                  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                 T1 T2 T3 T4
  17Q GAIN MUTATED   18  9 11  4
  17Q GAIN WILD-TYPE 50 32 31  4
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               18                 50
  T2                9                 32
  T3               11                 31
  T4                4                  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"
D31V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   23  0
  17Q GAIN WILD-TYPE 79  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     23    0
  17Q GAIN WILD-TYPE   79    3
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               23                 79
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17Q GAIN MUTATED   27  2 13
  17Q GAIN WILD-TYPE 93  1 24
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               27                 93
  M1                2                  1
  MX               13                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   12 30
  17Q GAIN WILD-TYPE 48 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12   30
  17Q GAIN WILD-TYPE   48   70
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               12                 48
  MALE                 30                 70
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17Q GAIN MUTATED                         0                       42
  17Q GAIN WILD-TYPE                       2                      114
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17Q GAIN MUTATED                                  0
  17Q GAIN WILD-TYPE                                2
D31V8, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       42                114
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    31   5   1   5
  17Q GAIN WILD-TYPE 100   6   0   7
D31V9, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               31                100
  R1                5                  6
  R2                1                  0
  RX                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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0    16
  17Q GAIN WILD-TYPE                                1    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           4    20
  17Q GAIN WILD-TYPE                         4    89
D31V10, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          16                 20
  BLACK OR AFRICAN AMERICAN                       4                  4
  WHITE                                          20                 89
[1] 4 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     1  39
  17Q GAIN WILD-TYPE   2 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   39
  17Q GAIN WILD-TYPE    2  104
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               39                104
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    7  3
  18P GAIN WILD-TYPE 84 63
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                147 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 63 
$`18P GAIN MUTATED`
TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN TCGA-ED-A66X 
        4.24         0.13        79.73         7.33        29.56        13.35 
TCGA-EP-A3JL TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
        9.96        60.36        51.06        58.49 

$`18P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-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-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         0.07         2.86         0.39         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.10         0.07         0.10        37.78        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-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
      100.96        13.41        12.69        15.85        13.91         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        11.74        10.98         0.62        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38         0.13         0.03         0.33         0.39         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57         5.10        14.24        12.85         8.71         1.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  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 
            21.455             13.910 
[1] "0.1 - 79.7 (21.5)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.8"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P GAIN MUTATED         2        2         0          5          0
  18P GAIN WILD-TYPE      63       35         2         26          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P GAIN MUTATED            0        1         0         0
  18P GAIN WILD-TYPE          5        0         1         2
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   2                 63
  STAGE II                  2                 35
  STAGE III                 0                  2
  STAGE IIIA                5                 26
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  1                  0
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18P GAIN MUTATED    2  2  6  0
  18P GAIN WILD-TYPE 66 39 36  8
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                2                 66
  T2                2                 39
  T3                6                 36
  T4                0                  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"
D32V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    8  0
  18P GAIN WILD-TYPE 94  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8    0
  18P GAIN WILD-TYPE   94    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                8                 94
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18P GAIN MUTATED     8   1   1
  18P GAIN WILD-TYPE 112   2  36
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                8                112
  M1                1                  2
  MX                1                 36
[1] 3 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    3  7
  18P GAIN WILD-TYPE 57 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    7
  18P GAIN WILD-TYPE   57   93
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 57
  MALE                  7                 93
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18P GAIN MUTATED                         0                       10
  18P GAIN WILD-TYPE                       2                      146
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18P GAIN MUTATED                                  0
  18P GAIN WILD-TYPE                                2
D32V8, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       10                146
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED     6   1   1   1
  18P GAIN WILD-TYPE 125  10   0  11
D32V9, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                6                125
  R1                1                 10
  R2                1                  0
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     5
  18P GAIN WILD-TYPE                                1    31
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           0     5
  18P GAIN WILD-TYPE                         8   104
D32V10, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 31
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                           5                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"
D32V11, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  10
  18P GAIN WILD-TYPE   3 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   10
  18P GAIN WILD-TYPE    3  133
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               10                133
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    6  3
  18Q GAIN WILD-TYPE 85 63
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                148 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 63 
$`18Q GAIN MUTATED`
TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN TCGA-EP-A3JL 
        4.24         0.13        79.73         7.33        29.56         9.96 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
       60.36        51.06        58.49 

$`18Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-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-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         0.07         2.86         0.39         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.10         0.07         0.10        37.78        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-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 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-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
        8.12         6.38         0.13         0.03         0.33         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-A7M7 TCGA-G3-A7M9 
       11.97         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        1.71        58.88        16.37         4.44 

  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 
            29.560             13.875 
[1] "0.1 - 79.7 (29.6)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.7"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18Q GAIN MUTATED         2        2         0          4          0
  18Q GAIN WILD-TYPE      63       35         2         27          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q GAIN MUTATED            0        1         0         0
  18Q GAIN WILD-TYPE          5        0         1         2
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   2                 63
  STAGE II                  2                 35
  STAGE III                 0                  2
  STAGE IIIA                4                 27
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  1                  0
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18Q GAIN MUTATED    2  2  5  0
  18Q GAIN WILD-TYPE 66 39 37  8
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                2                 66
  T2                2                 39
  T3                5                 37
  T4                0                  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"
D33V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    7  0
  18Q GAIN WILD-TYPE 95  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7    0
  18Q GAIN WILD-TYPE   95    3
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                7                 95
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18Q GAIN MUTATED     7   1   1
  18Q GAIN WILD-TYPE 113   2  36
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                7                113
  M1                1                  2
  MX                1                 36
[1] 3 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    3  6
  18Q GAIN WILD-TYPE 57 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    6
  18Q GAIN WILD-TYPE   57   94
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                3                 57
  MALE                  6                 94
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18Q GAIN MUTATED                         0                        9
  18Q GAIN WILD-TYPE                       2                      147
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18Q GAIN MUTATED                                  0
  18Q GAIN WILD-TYPE                                2
D33V8, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                        9                147
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     5   1   1   1
  18Q GAIN WILD-TYPE 126  10   0  11
D33V9, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                5                126
  R1                1                 10
  R2                1                  0
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     4
  18Q GAIN WILD-TYPE                                1    32
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           0     5
  18Q GAIN WILD-TYPE                         8   104
D33V10, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                 32
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                           5                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"
D33V11, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   9
  18Q GAIN WILD-TYPE   3 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    9
  18Q GAIN WILD-TYPE    3  134
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                9                134
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   16 15
  19P GAIN WILD-TYPE 75 51
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                31                126 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                15                 51 
$`19P GAIN MUTATED`
TCGA-BC-A10Q TCGA-CC-5261 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 
       37.32         0.39        79.73       113.00         7.33        90.71 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A7 TCGA-DD-A3A9 
       19.79        12.95        21.14        55.69        13.78        30.61 
TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73G 
       73.38        29.56        73.81        12.26        66.35       100.96 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
        0.23         0.20         0.20        10.98         0.62        22.85 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M7 
       32.45        27.88        51.06        58.49         4.37         5.98 
TCGA-KR-A7K2 
       11.84 

$`19P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
       12.72         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        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       15.06        39.78        56.25        93.67         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-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
       13.41        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
        9.96        11.93        14.40        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-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.99         7.76         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        2.14        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         8.71         1.71        58.88        16.37         4.44 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.20               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            113.00             107.11 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            22.850             13.525 
[1] "0.2 - 113.0 (22.9)" "0.0 - 107.1 (13.5)"
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P GAIN MUTATED        13       10         0          4          1
  19P GAIN WILD-TYPE      52       27         2         27          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P GAIN MUTATED            0        1         1         1
  19P GAIN WILD-TYPE          5        0         0         1
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  13                 52
  STAGE II                 10                 27
  STAGE III                 0                  2
  STAGE IIIA                4                 27
  STAGE IIIB                1                  4
  STAGE IIIC                0                  5
  STAGE IV                  1                  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                 T1 T2 T3 T4
  19P GAIN MUTATED   14 11  6  1
  19P GAIN WILD-TYPE 54 30 36  7
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               14                 54
  T2               11                 30
  T3                6                 36
  T4                1                  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"
D34V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   21  1
  19P GAIN WILD-TYPE 81  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     21    1
  19P GAIN WILD-TYPE   81    2
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               21                 81
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19P GAIN MUTATED   24  2  6
  19P GAIN WILD-TYPE 96  1 31
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               24                 96
  M1                2                  1
  MX                6                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   16 16
  19P GAIN WILD-TYPE 44 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     16   16
  19P GAIN WILD-TYPE   44   84
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               16                 44
  MALE                 16                 84
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19P GAIN MUTATED                         0                       30
  19P GAIN WILD-TYPE                       2                      126
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19P GAIN MUTATED                                  2
  19P GAIN WILD-TYPE                                0
D34V8, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       30                126
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    29   1   1   1
  19P GAIN WILD-TYPE 102  10   0  11
D34V9, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               29                102
  R1                1                 10
  R2                1                  0
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     6
  19P GAIN WILD-TYPE                                1    30
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           1    24
  19P GAIN WILD-TYPE                         7    85
D34V10, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 30
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                          24                 85
[1] 4 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     1  29
  19P GAIN WILD-TYPE   2 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   29
  19P GAIN WILD-TYPE    2  114
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               29                114
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   20 16
  19Q GAIN WILD-TYPE 71 50
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                36                121 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                16                 50 
$`19Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-CC-5261 TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A118 
       37.32        10.13         0.39         0.10        79.73       113.00 
TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A39V 
        7.33        90.71        19.79        12.95        45.11        21.14 
TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       55.69        30.61        73.38        29.56        73.81        12.26 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KB 
       66.35       100.96         0.23         0.20         0.20        10.98 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T 
        0.62        22.85        32.45        27.88         0.39        51.06 
TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-KR-A7K2 TCGA-MI-A75G TCGA-NI-A8LF 
       58.49         4.37         5.98        11.84        14.24        16.37 

$`19Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-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        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       56.25        93.67         0.30        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A8O5 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-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        19.10         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33        60.36         1.22        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M9 
       19.23        14.70        11.97         7.99         7.76         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG 
        1.02         2.66         4.01         2.14        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57         5.10        12.85         8.71         1.71        58.88 
TCGA-O8-A75V 
        4.44 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.10               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            113.00             107.11 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            20.465             13.640 
[1] "0.1 - 113.0 (20.5)" "0.0 - 107.1 (13.6)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED        16       11         0          5          0
  19Q GAIN WILD-TYPE      49       26         2         26          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q GAIN MUTATED            0        1         1         1
  19Q GAIN WILD-TYPE          5        0         0         1
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  16                 49
  STAGE II                 11                 26
  STAGE III                 0                  2
  STAGE IIIA                5                 26
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  1                  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                 T1 T2 T3 T4
  19Q GAIN MUTATED   17 12  7  1
  19Q GAIN WILD-TYPE 51 29 35  7
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               17                 51
  T2               12                 29
  T3                7                 35
  T4                1                  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"
D35V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   23  1
  19Q GAIN WILD-TYPE 79  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     23    1
  19Q GAIN WILD-TYPE   79    2
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               23                 79
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19Q GAIN MUTATED   27  2  8
  19Q GAIN WILD-TYPE 93  1 29
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               27                 93
  M1                2                  1
  MX                8                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   17 20
  19Q GAIN WILD-TYPE 43 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     17   20
  19Q GAIN WILD-TYPE   43   80
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               17                 43
  MALE                 20                 80
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19Q GAIN MUTATED                         0                       35
  19Q GAIN WILD-TYPE                       2                      121
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19Q GAIN MUTATED                                  2
  19Q GAIN WILD-TYPE                                0
D35V8, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       35                121
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED   34  1  1  1
  19Q GAIN WILD-TYPE 97 10  0 11
D35V9, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               34                 97
  R1                1                 10
  R2                1                  0
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     7
  19Q GAIN WILD-TYPE                                1    29
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           1    29
  19Q GAIN WILD-TYPE                         7    80
D35V10, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 29
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                          29                 80
[1] 4 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     1  35
  19Q GAIN WILD-TYPE   2 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   35
  19Q GAIN WILD-TYPE    2  108
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               35                108
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   24 23
  20P GAIN WILD-TYPE 67 43
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                47                110 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                23                 43 
$`20P GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H 
       48.99        37.32        10.13        13.84         0.26        14.60 
TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        0.39         0.10         0.10       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V 
        0.46        12.95        45.11        49.15        29.16        21.14 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NR 
      102.74        13.78        30.61        73.38        29.56         0.30 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KB 
       66.35       100.96        13.35         0.23         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-A7M9 TCGA-HP-A5MZ 
       58.49        14.86         4.37         7.76         1.84         2.66 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A8LF 
       11.84        13.38         0.49        14.24        16.37 

$`20P GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        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-A3KG 
       23.34         1.12        69.57         5.03        44.42        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
        9.50        12.72         0.07         2.86         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.07         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       19.79        75.65         6.71         6.02        18.35        13.64 
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-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       17.59        20.12       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 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       73.81        93.67        12.26        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       15.85        13.91         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 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-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        19.10        27.88         8.12         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33        60.36        51.06        53.79        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-A5SL TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-K7-A6G5 
       14.70        11.97         7.99         5.98         1.02         4.01 
TCGA-KR-A7K0 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        2.14         9.57         5.10        12.85         8.71         1.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.10               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            113.00             107.11 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             13.35              14.55 
[1] "0.1 - 113.0 (13.3)" "0.0 - 107.1 (14.6)"
[1] "hr=" "1.3"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED        19       11         2          8          3
  20P GAIN WILD-TYPE      46       26         0         23          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P GAIN MUTATED            1        1         0         1
  20P GAIN WILD-TYPE          4        0         1         1
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  19                 46
  STAGE II                 11                 26
  STAGE III                 2                  0
  STAGE IIIA                8                 23
  STAGE IIIB                3                  2
  STAGE IIIC                1                  4
  STAGE IV                  1                  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                 T1 T2 T3 T4
  20P GAIN MUTATED   20 12 15  1
  20P GAIN WILD-TYPE 48 29 27  7
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               20                 48
  T2               12                 29
  T3               15                 27
  T4                1                  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"
D36V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   31  1
  20P GAIN WILD-TYPE 71  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     31    1
  20P GAIN WILD-TYPE   71    2
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               31                 71
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED   38  2  8
  20P GAIN WILD-TYPE 82  1 29
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               38                 82
  M1                2                  1
  MX                8                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   21 27
  20P GAIN WILD-TYPE 39 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     21   27
  20P GAIN WILD-TYPE   39   73
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               21                 39
  MALE                 27                 73
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20P GAIN MUTATED                         0                       47
  20P GAIN WILD-TYPE                       2                      109
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20P GAIN MUTATED                                  1
  20P GAIN WILD-TYPE                                1
D36V8, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       47                109
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   40  3  1  3
  20P GAIN WILD-TYPE 91  8  0  9
D36V9, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               40                 91
  R1                3                  8
  R2                1                  0
  RX                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0    10
  20P GAIN WILD-TYPE                                1    26
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           1    35
  20P GAIN WILD-TYPE                         7    74
D36V10, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          10                 26
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                          35                 74
[1] 4 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     0  42
  20P GAIN WILD-TYPE   3 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0   42
  20P GAIN WILD-TYPE    3  101
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               42                101
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   26 23
  20Q GAIN WILD-TYPE 65 43
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                49                108 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                23                 43 
$`20Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H 
       48.99        37.32        10.13        13.84         0.26        14.60 
TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A118 TCGA-DD-A119 
        0.39         0.10         0.10         0.13       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
        2.60         0.46        21.76        12.95        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND 
       29.16        21.14       102.74        13.78        30.61        73.38 
TCGA-DD-A4NN TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A66Y 
       29.56         0.30        66.35       100.96        13.35         0.23 
TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 
        0.20        10.98         9.96        22.85        32.45         6.38 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SM TCGA-G3-A6UC 
        0.39         1.22        58.49        14.86         4.37         7.76 
TCGA-G3-A7M9 TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G 
        1.84         2.66        11.84        13.38         0.49        14.24 
TCGA-NI-A8LF 
       16.37 

$`20Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        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-A3KG 
       23.34         1.12        69.57         5.03        44.42        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
        9.50        12.72         0.07         2.86         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        3.32         0.07        79.73        37.78        83.57        53.33 
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-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
        6.71         6.02        18.35        13.64        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      107.11         0.36        33.14        32.52        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       18.44        15.06        39.78        56.25        73.81        93.67 
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-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
        1.45        27.72        13.41        12.69        15.85        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       19.99        11.74         0.62        11.93        14.40        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         8.12         0.13         0.03         0.33        60.36 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
       51.06        53.79        28.27        30.74        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-A7M7 TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-MI-A75C 
        7.99         5.98         1.02         4.01         2.14         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        12.85         8.71         1.71        58.88         4.44 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.10               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            113.00             107.11 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             13.35              14.55 
[1] "0.1 - 113.0 (13.3)" "0.0 - 107.1 (14.6)"
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED        20       11         2          9          3
  20Q GAIN WILD-TYPE      45       26         0         22          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q GAIN MUTATED            1        1         0         1
  20Q GAIN WILD-TYPE          4        0         1         1
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  20                 45
  STAGE II                 11                 26
  STAGE III                 2                  0
  STAGE IIIA                9                 22
  STAGE IIIB                3                  2
  STAGE IIIC                1                  4
  STAGE IV                  1                  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                 T1 T2 T3 T4
  20Q GAIN MUTATED   21 12 16  1
  20Q GAIN WILD-TYPE 47 29 26  7
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               21                 47
  T2               12                 29
  T3               16                 26
  T4                1                  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"
D37V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   33  1
  20Q GAIN WILD-TYPE 69  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     33    1
  20Q GAIN WILD-TYPE   69    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               33                 69
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   40  2  8
  20Q GAIN WILD-TYPE 80  1 29
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               40                 80
  M1                2                  1
  MX                8                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   21 29
  20Q GAIN WILD-TYPE 39 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     21   29
  20Q GAIN WILD-TYPE   39   71
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               21                 39
  MALE                 29                 71
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20Q GAIN MUTATED                         0                       49
  20Q GAIN WILD-TYPE                       2                      107
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20Q GAIN MUTATED                                  1
  20Q GAIN WILD-TYPE                                1
D37V8, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       49                107
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED   41  3  1  4
  20Q GAIN WILD-TYPE 90  8  0  8
D37V9, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               41                 90
  R1                3                  8
  R2                1                  0
  RX                4                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0    11
  20Q GAIN WILD-TYPE                                1    25
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           1    36
  20Q GAIN WILD-TYPE                         7    73
D37V10, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          11                 25
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                          36                 73
[1] 4 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    0 44
  20Q GAIN WILD-TYPE  3 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0   44
  20Q GAIN WILD-TYPE    3   99
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               44                 99
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    8  5
  21Q GAIN WILD-TYPE 83 61
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                13                144 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 61 
$`21Q GAIN MUTATED`
TCGA-BC-A217 TCGA-CC-5261 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A3A5 TCGA-DD-A4NV 
       13.84         0.39         4.24        79.73       102.74        66.35 
TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A3CG 
        0.20        10.98        22.85        27.88        51.06        22.13 
TCGA-MI-A75G 
       14.24 

$`21Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        44.42         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
       12.72         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        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       73.81        93.67        12.26         0.30        80.75        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         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-A2HT 
       19.99        11.74         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-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-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         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         8.71         1.71        58.88        16.37         4.44 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.20               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            102.74             113.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             22.13              13.71 
[1] "0.2 - 102.7 (22.1)" "0.0 - 113.0 (13.7)"
[1] "hr=" "1.5"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  21Q GAIN MUTATED         4        5         1          4          0
  21Q GAIN WILD-TYPE      61       32         1         27          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q GAIN MUTATED            0        0         0         0
  21Q GAIN WILD-TYPE          5        1         1         2
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   4                 61
  STAGE II                  5                 32
  STAGE III                 1                  1
  STAGE IIIA                4                 27
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  21Q GAIN MUTATED    4  5  5  0
  21Q GAIN WILD-TYPE 64 36 37  8
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                4                 64
  T2                5                 36
  T3                5                 37
  T4                0                  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"
D38V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    9  0
  21Q GAIN WILD-TYPE 93  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9    0
  21Q GAIN WILD-TYPE   93    3
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                9                 93
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  21Q GAIN MUTATED    11   0   3
  21Q GAIN WILD-TYPE 109   3  34
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0               11                109
  M1                0                  3
  MX                3                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    7  7
  21Q GAIN WILD-TYPE 53 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7    7
  21Q GAIN WILD-TYPE   53   93
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                7                 53
  MALE                  7                 93
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  21Q GAIN MUTATED                         0                       13
  21Q GAIN WILD-TYPE                       2                      143
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  21Q GAIN MUTATED                                  1
  21Q GAIN WILD-TYPE                                1
D38V8, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       13                143
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    10   1   0   3
  21Q GAIN WILD-TYPE 121  10   1   9
D38V9, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               10                121
  R1                1                 10
  R2                0                  1
  RX                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     3
  21Q GAIN WILD-TYPE                                1    33
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           0    11
  21Q GAIN WILD-TYPE                         8    98
D38V10, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                 33
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                          11                 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"
D38V11, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  13
  21Q GAIN WILD-TYPE   3 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   13
  21Q GAIN WILD-TYPE    3  130
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               13                130
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   12  7
  22Q GAIN WILD-TYPE 79 59
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                138 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                 59 
$`22Q GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A3MB 
       10.13         5.03        14.60         0.07         0.39         0.10 
TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1EJ TCGA-DD-A4ND TCGA-DD-A73G TCGA-ED-A66X 
      113.00        51.29        29.16        73.38       100.96        13.35 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-G3-A25X 
        0.20         0.20        22.85        19.10        27.88        58.49 
TCGA-G3-A3CG 
       22.13 

$`22Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5260 
       13.84         0.26        22.36         9.50        12.72         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        3.39         4.24         3.32         0.10         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        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-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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.07        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       27.72        13.41        12.69        15.85        13.91         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       32.45         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        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         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         8.71         1.71        58.88        16.37         4.44 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            113.00             107.11 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             19.10              13.81 
[1] "0.1 - 113.0 (19.1)" "0.0 - 107.1 (13.8)"
[1] "hr=" "1.5"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  22Q GAIN MUTATED         6        7         0          3          0
  22Q GAIN WILD-TYPE      59       30         2         28          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q GAIN MUTATED            1        0         0         0
  22Q GAIN WILD-TYPE          4        1         1         2
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   6                 59
  STAGE II                  7                 30
  STAGE III                 0                  2
  STAGE IIIA                3                 28
  STAGE IIIB                0                  5
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  22Q GAIN MUTATED    7  7  5  0
  22Q GAIN WILD-TYPE 61 34 37  8
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                7                 61
  T2                7                 34
  T3                5                 37
  T4                0                  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"
D39V5, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   12  1
  22Q GAIN WILD-TYPE 90  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     12    1
  22Q GAIN WILD-TYPE   90    2
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               12                 90
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  22Q GAIN MUTATED    16   0   3
  22Q GAIN WILD-TYPE 104   3  34
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               16                104
  M1                0                  3
  MX                3                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    8 11
  22Q GAIN WILD-TYPE 52 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      8   11
  22Q GAIN WILD-TYPE   52   89
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                8                 52
  MALE                 11                 89
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  22Q GAIN MUTATED                         0                       18
  22Q GAIN WILD-TYPE                       2                      138
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  22Q GAIN MUTATED                                  1
  22Q GAIN WILD-TYPE                                1
D39V8, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       18                138
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    15   1   0   3
  22Q GAIN WILD-TYPE 116  10   1   9
D39V9, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               15                116
  R1                1                 10
  R2                0                  1
  RX                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     7
  22Q GAIN WILD-TYPE                                1    29
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           0    12
  22Q GAIN WILD-TYPE                         8    97
D39V10, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 29
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                          12                 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"
D39V11, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  19
  22Q GAIN WILD-TYPE   3 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   19
  22Q GAIN WILD-TYPE    3  124
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               19                124
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   18  9
  XQ GAIN WILD-TYPE 73 57
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               27               130 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9                57 
$`XQ GAIN MUTATED`
TCGA-BC-A10U TCGA-BC-A10Z TCGA-BC-A3KF TCGA-CC-5260 TCGA-DD-A11A TCGA-DD-A39V 
       27.52         1.12         0.26         2.86         2.60        21.14 
TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NV TCGA-DD-A73D 
       17.59        13.78        14.07        39.78        66.35        10.98 
TCGA-DD-A73G TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A4ZQ 
      100.96        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-K7-A6G5 
       53.79        22.13        19.53        14.70         7.99         4.01 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-O8-A75V 
        0.49        14.24         4.44 

$`XQ GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32        23.34        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       13.84        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-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-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-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       32.52        73.38        14.24        18.44        15.06        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 
       10.98         9.30         7.56         1.45        27.72        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A26S 
        0.20         0.20         0.20         0.20         0.20        19.99 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
       10.98         0.62        11.93        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       60.36         1.22        51.06        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ 
       14.86        21.53        25.64         5.92        19.23        11.97 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
        2.14        11.84        13.38         9.57         5.10        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
        8.71         1.71        58.88        16.37 

  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 
           14.070            13.875 
[1] "0.3 - 101.0 (14.1)" "0.0 - 113.0 (13.9)"
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ GAIN MUTATED        14        6         0          5          1          1
  XQ GAIN WILD-TYPE      51       31         2         26          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ GAIN MUTATED          0         0         0
  XQ GAIN WILD-TYPE        1         1         2
D40V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 14                51
  STAGE II                 6                31
  STAGE III                0                 2
  STAGE IIIA               5                26
  STAGE IIIB               1                 4
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ GAIN MUTATED   14  7  6  1
  XQ GAIN WILD-TYPE 54 34 36  7
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              14                54
  T2               7                34
  T3               6                36
  T4               1                 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"
D40V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   16  0
  XQ GAIN WILD-TYPE 86  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     16    0
  XQ GAIN WILD-TYPE   86    3
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              16                86
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  XQ GAIN MUTATED    19   0   9
  XQ GAIN WILD-TYPE 101   3  28
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              19               101
  M1               0                 3
  MX               9                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"
D40V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    9 19
  XQ GAIN WILD-TYPE 51 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      9   19
  XQ GAIN WILD-TYPE   51   81
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               9                51
  MALE                19                81
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XQ GAIN MUTATED                         0                       28
  XQ GAIN WILD-TYPE                       2                      128
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XQ GAIN MUTATED                                  0
  XQ GAIN WILD-TYPE                                2
D40V8, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      28               128
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    21   3   0   3
  XQ GAIN WILD-TYPE 110   8   1   9
D40V9, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              21               110
  R1               3                 8
  R2               0                 1
  RX               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  1     5
  XQ GAIN WILD-TYPE                                0    31
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           2    18
  XQ GAIN WILD-TYPE                         6    91
D40V10, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          5                31
  BLACK OR AFRICAN AMERICAN                      2                 6
  WHITE                                         18                91
[1] 4 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  25
  XQ GAIN WILD-TYPE   2 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   25
  XQ GAIN WILD-TYPE    2  118
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              25               118
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   23 14
  1P LOSS WILD-TYPE 68 52
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               37               120 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               14                52 
$`1P LOSS MUTATED`
TCGA-BC-A10S TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A3MB 
       46.78        13.84        14.60         0.07         0.39         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A1E9 
        0.13        79.73       113.00         7.33         0.46        90.71 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A3A1 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NN 
       49.15        29.16         7.66        30.61        14.24        29.56 
TCGA-DD-A73B TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 
        9.30        13.35         0.23         0.20         0.20         0.20 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZP 
       10.98         0.62        22.85        27.88         0.33        60.36 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM 
       53.79        58.49        14.86        14.70         7.99         4.37 
TCGA-KR-A7K2 
       11.84 

$`1P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5260 
       44.42         0.26        22.36         9.50        12.72         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-A39X TCGA-DD-A39Y 
        6.02        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81        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-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO 
       14.07        18.44        15.06        39.78        56.25        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP 
       12.69        15.85        13.91         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        11.74         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         8.12         6.38         0.13         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
        0.39         1.22        51.06        28.27        30.74        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-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        2.14        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         8.71         1.71        58.88        16.37         4.44 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           113.00            107.11 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           13.350            14.155 
[1] "0.1 - 113.0 (13.3)" "0.0 - 107.1 (14.2)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P LOSS MUTATED        11       11         1          9          1          1
  1P LOSS WILD-TYPE      54       26         1         22          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P LOSS MUTATED          1         1         1
  1P LOSS WILD-TYPE        0         0         1
D41V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 11                54
  STAGE II                11                26
  STAGE III                1                 1
  STAGE IIIA               9                22
  STAGE IIIB               1                 4
  STAGE IIIC               1                 4
  STAGE IV                 1                 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                T1 T2 T3 T4
  1P LOSS MUTATED   13 11 13  1
  1P LOSS WILD-TYPE 55 30 29  7
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              13                55
  T2              11                30
  T3              13                29
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   24  2
  1P LOSS WILD-TYPE 78  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     24    2
  1P LOSS WILD-TYPE   78    1
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              24                78
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED   31  2  5
  1P LOSS WILD-TYPE 89  1 32
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              31                89
  M1               2                 1
  MX               5                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   17 21
  1P LOSS WILD-TYPE 43 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     17   21
  1P LOSS WILD-TYPE   43   79
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              17                43
  MALE                21                79
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1P LOSS MUTATED                         0                       36
  1P LOSS WILD-TYPE                       2                      120
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1P LOSS MUTATED                                  2
  1P LOSS WILD-TYPE                                0
D41V8, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      36               120
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED   33  1  1  3
  1P LOSS WILD-TYPE 98 10  0  9
D41V9, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              33                98
  R1               1                10
  R2               1                 0
  RX               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0    14
  1P LOSS WILD-TYPE                                1    22
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           1    22
  1P LOSS WILD-TYPE                         7    87
D41V10, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                22
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                         22                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1  34
  1P LOSS WILD-TYPE   2 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   34
  1P LOSS WILD-TYPE    2  109
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              34               109
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    7  5
  1Q LOSS WILD-TYPE 84 61
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               145 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5                61 
$`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-ED-A82E TCGA-ED-A8O5 TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25U 
        7.66         0.20         0.20        22.85        60.36        53.79 

$`1Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-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-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-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-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         2.60        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-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15         6.02        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        19.76        25.81        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        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-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         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       14.24        12.85         8.71         1.71        58.88        16.37 
TCGA-O8-A75V 
        4.44 

  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 
            10.75             14.07 
[1] "0.1 - 60.4 (10.8)"  "0.0 - 113.0 (14.1)"
[1] "hr=" "1.2"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q LOSS MUTATED         3        2         0          5          0          1
  1Q LOSS WILD-TYPE      62       35         2         26          5          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q LOSS MUTATED          0         1         0
  1Q LOSS WILD-TYPE        1         0         2
D42V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  3                62
  STAGE II                 2                35
  STAGE III                0                 2
  STAGE IIIA               5                26
  STAGE IIIB               0                 5
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                1                 0
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1Q LOSS MUTATED    5  2  6  0
  1Q LOSS WILD-TYPE 63 39 36  8
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               5                63
  T2               2                39
  T3               6                36
  T4               0                 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"
D42V5, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    7  2
  1Q LOSS WILD-TYPE 95  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      7    2
  1Q LOSS WILD-TYPE   95    1
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               7                95
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1Q LOSS MUTATED    10   0   3
  1Q LOSS WILD-TYPE 110   3  34
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0              10               110
  M1               0                 3
  MX               3                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    5  8
  1Q LOSS WILD-TYPE 55 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      5    8
  1Q LOSS WILD-TYPE   55   92
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               5                55
  MALE                 8                92
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1Q LOSS MUTATED                         0                       13
  1Q LOSS WILD-TYPE                       2                      143
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1Q LOSS MUTATED                                  0
  1Q LOSS WILD-TYPE                                2
D42V8, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      13               143
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    10   1   0   2
  1Q LOSS WILD-TYPE 121  10   1  10
D42V9, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              10               121
  R1               1                10
  R2               0                 1
  RX               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     5
  1Q LOSS WILD-TYPE                                1    31
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           0     7
  1Q LOSS WILD-TYPE                         8   102
D42V10, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          5                31
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          7               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  11
  1Q LOSS WILD-TYPE   3 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   11
  1Q LOSS WILD-TYPE    3  132
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              11               132
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    9  4
  2P LOSS WILD-TYPE 82 62
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               13               144 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                62 
$`2P LOSS MUTATED`
TCGA-BC-A10Y TCGA-BC-A3KF TCGA-BC-A69H TCGA-DD-A11C TCGA-DD-A39Y TCGA-ED-A459 
       23.34         0.26        14.60        21.76         5.62        13.41 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-FV-A3I1 TCGA-G3-A25S TCGA-G3-A5SM 
        0.23         0.20         0.20         8.12         1.22         4.37 
TCGA-KR-A7K2 
       11.84 

$`2P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
       27.52         2.99        25.32         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 
       44.42        13.84        22.36         9.50        12.72         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        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
      100.96        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10        27.88         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33        60.36         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-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         7.99 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        2.14        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         8.71         1.71        58.88        16.37         4.44 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.20              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            23.34            113.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             5.62             14.32 
[1] "0.2 - 23.3 (5.6)"   "0.0 - 113.0 (14.3)"
[1] "hr=" "2"  
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P LOSS MUTATED         6        6         0          1          0          0
  2P LOSS WILD-TYPE      59       31         2         30          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P LOSS MUTATED          0         0         0
  2P LOSS WILD-TYPE        1         1         2
D43V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  6                59
  STAGE II                 6                31
  STAGE III                0                 2
  STAGE IIIA               1                30
  STAGE IIIB               0                 5
  STAGE IIIC               0                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2P LOSS MUTATED    6  6  1  1
  2P LOSS WILD-TYPE 62 35 41  7
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               6                62
  T2               6                35
  T3               1                41
  T4               1                 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"
D43V5, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    6  0
  2P LOSS WILD-TYPE 96  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    0
  2P LOSS WILD-TYPE   96    3
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               6                96
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2P LOSS MUTATED    11   0   3
  2P LOSS WILD-TYPE 109   3  34
D43V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0              11               109
  M1               0                 3
  MX               3                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    4 10
  2P LOSS WILD-TYPE 56 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4   10
  2P LOSS WILD-TYPE   56   90
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               4                56
  MALE                10                90
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2P LOSS MUTATED                         0                       13
  2P LOSS WILD-TYPE                       2                      143
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2P LOSS MUTATED                                  1
  2P LOSS WILD-TYPE                                1
D43V8, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      13               143
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    11   1   0   2
  2P LOSS WILD-TYPE 120  10   1  10
D43V9, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              11               120
  R1               1                10
  R2               0                 1
  RX               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     5
  2P LOSS WILD-TYPE                                1    31
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           0     9
  2P LOSS WILD-TYPE                         8   100
D43V10, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          5                31
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          9               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  12
  2P LOSS WILD-TYPE   3 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   12
  2P LOSS WILD-TYPE    3  131
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              12               131
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    8  5
  2Q LOSS WILD-TYPE 83 61
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               144 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                61 
$`2Q LOSS MUTATED`
TCGA-BC-A10Y TCGA-BC-A3KF TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A39Y TCGA-DD-A4NJ 
       23.34         0.26        83.57        21.76         5.62        15.06 
TCGA-DD-A73B TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-FV-A3I1 
        9.30        13.41         0.23         0.20         0.20         8.12 
TCGA-KR-A7K2 
       11.84 

$`2Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
       27.52         2.99        25.32         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-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        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       14.24        18.44        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72       100.96        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-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         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        2.14        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         8.71         1.71        58.88        16.37         4.44 

  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 
             9.30             14.24 
[1] "0.2 - 83.6 (9.3)"   "0.0 - 113.0 (14.2)"
[1] "hr=" "1.5"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q LOSS MUTATED         6        5         0          3          0          0
  2Q LOSS WILD-TYPE      59       32         2         28          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q LOSS MUTATED          0         0         0
  2Q LOSS WILD-TYPE        1         1         2
D44V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  6                59
  STAGE II                 5                32
  STAGE III                0                 2
  STAGE IIIA               3                28
  STAGE IIIB               0                 5
  STAGE IIIC               0                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2Q LOSS MUTATED    6  5  3  1
  2Q LOSS WILD-TYPE 62 36 39  7
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               6                62
  T2               5                36
  T3               3                39
  T4               1                 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"
D44V5, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    9  0
  2Q LOSS WILD-TYPE 93  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      9    0
  2Q LOSS WILD-TYPE   93    3
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               9                93
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2Q LOSS MUTATED    12   0   3
  2Q LOSS WILD-TYPE 108   3  34
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0              12               108
  M1               0                 3
  MX               3                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    6  9
  2Q LOSS WILD-TYPE 54 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      6    9
  2Q LOSS WILD-TYPE   54   91
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               6                54
  MALE                 9                91
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2Q LOSS MUTATED                         0                       14
  2Q LOSS WILD-TYPE                       2                      142
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2Q LOSS MUTATED                                  1
  2Q LOSS WILD-TYPE                                1
D44V8, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      14               142
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    12   0   0   3
  2Q LOSS WILD-TYPE 119  11   1   9
D44V9, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              12               119
  R1               0                11
  R2               0                 1
  RX               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     6
  2Q LOSS WILD-TYPE                                1    30
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           0     9
  2Q LOSS WILD-TYPE                         8   100
D44V10, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                30
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          9               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1  11
  2Q LOSS WILD-TYPE   2 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   11
  2Q LOSS WILD-TYPE    2  132
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              11               132
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   17  5
  3P LOSS WILD-TYPE 74 61
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22               135 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                61 
$`3P LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 
       10.13         5.03         4.24         0.07         0.10        79.73 
TCGA-DD-A118 TCGA-DD-A1E9 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NO 
      113.00        90.71        30.61        33.14        18.44        73.81 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-FV-A3I0 TCGA-G3-A25T 
        0.23         0.20         0.20         0.20        27.88        51.06 
TCGA-G3-A25X TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MR-A8JO 
       58.49        11.84        13.38         1.71 

$`3P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-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 
       14.07        14.24        15.06        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       13.41        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10         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-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         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           113.00            107.11 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            12.61             14.07 
[1] "0.1 - 113.0 (12.6)" "0.0 - 107.1 (14.1)"
[1] "hr=" "2.5"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P LOSS MUTATED         4        8         0          6          0          1
  3P LOSS WILD-TYPE      61       29         2         25          5          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P LOSS MUTATED          0         0         1
  3P LOSS WILD-TYPE        1         1         1
D45V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  4                61
  STAGE II                 8                29
  STAGE III                0                 2
  STAGE IIIA               6                25
  STAGE IIIB               0                 5
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    4  9  8  1
  3P LOSS WILD-TYPE 64 32 34  7
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               4                64
  T2               9                32
  T3               8                34
  T4               1                 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"
D45V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   15  1
  3P LOSS WILD-TYPE 87  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     15    1
  3P LOSS WILD-TYPE   87    2
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              15                87
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3P LOSS MUTATED    18   1   3
  3P LOSS WILD-TYPE 102   2  34
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              18               102
  M1               1                 2
  MX               3                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   11 11
  3P LOSS WILD-TYPE 49 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     11   11
  3P LOSS WILD-TYPE   49   89
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              11                49
  MALE                11                89
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3P LOSS MUTATED                         1                       19
  3P LOSS WILD-TYPE                       1                      137
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3P LOSS MUTATED                                  2
  3P LOSS WILD-TYPE                                0
D45V8, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      19               137
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    20   0   0   2
  3P LOSS WILD-TYPE 111  11   1  10
D45V9, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              20               111
  R1               0                11
  R2               0                 1
  RX               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     8
  3P LOSS WILD-TYPE                                1    28
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           0    14
  3P LOSS WILD-TYPE                         8    95
D45V10, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                28
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                         14                95
[1] 4 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  19
  3P LOSS WILD-TYPE   3 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   19
  3P LOSS WILD-TYPE    3  124
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              19               124
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   11  2
  3Q LOSS WILD-TYPE 80 64
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13               144 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                64 
$`3Q LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1E9 TCGA-DD-A4NA TCGA-DD-A4NI 
        5.03        79.73       113.00        90.71        33.14        18.44 
TCGA-DD-A4NO TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E TCGA-KR-A7K2 TCGA-KR-A7K7 
       73.81         0.23         0.20         0.20        11.84        13.38 
TCGA-MR-A8JO 
        1.71 

$`3Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       12.72         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-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-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-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        30.61        32.52        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       14.24        15.06        39.78        56.25        29.56        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-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-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.66         4.01         2.14         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       14.24        12.85         8.71        58.88        16.37         4.44 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.20              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           113.00            107.11 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            13.38             13.99 
[1] "0.2 - 113.0 (13.4)" "0.0 - 107.1 (14.0)"
[1] "hr=" "4.6"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q LOSS MUTATED         4        5         0          2          0          1
  3Q LOSS WILD-TYPE      61       32         2         29          5          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q LOSS MUTATED          0         0         0
  3Q LOSS WILD-TYPE        1         1         2
D46V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  4                61
  STAGE II                 5                32
  STAGE III                0                 2
  STAGE IIIA               2                29
  STAGE IIIB               0                 5
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3Q LOSS MUTATED    4  6  3  0
  3Q LOSS WILD-TYPE 64 35 39  8
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               4                64
  T2               6                35
  T3               3                39
  T4               0                 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"
D46V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    9  1
  3Q LOSS WILD-TYPE 93  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      9    1
  3Q LOSS WILD-TYPE   93    2
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               9                93
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3Q LOSS MUTATED    11   0   2
  3Q LOSS WILD-TYPE 109   3  35
D46V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0              11               109
  M1               0                 3
  MX               2                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"
D46V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    6  7
  3Q LOSS WILD-TYPE 54 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6    7
  3Q LOSS WILD-TYPE   54   93
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               6                54
  MALE                 7                93
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3Q LOSS MUTATED                         1                       11
  3Q LOSS WILD-TYPE                       1                      145
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3Q LOSS MUTATED                                  1
  3Q LOSS WILD-TYPE                                1
D46V8, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      11               145
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    12   0   0   1
  3Q LOSS WILD-TYPE 119  11   1  11
D46V9, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              12               119
  R1               0                11
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     3
  3Q LOSS WILD-TYPE                                1    33
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           0    10
  3Q LOSS WILD-TYPE                         8    99
D46V10, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                33
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                         10                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"
D46V11, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  10
  3Q LOSS WILD-TYPE   3 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   10
  3Q LOSS WILD-TYPE    3  133
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              10               133
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   18 14
  4P LOSS WILD-TYPE 73 52
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               32               125 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               14                52 
$`4P LOSS MUTATED`
TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-A3MC 
       23.34         5.03        13.84         9.50        14.60         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       79.73        37.78         7.33        29.16        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-ED-A459 
        5.62        30.61        18.44        15.06        29.56        13.41 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A496 
       13.35         0.20         0.20        10.98         0.62         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A7M9 TCGA-KR-A7K2 
       60.36         1.22        53.79        58.49         1.84        11.84 
TCGA-KR-A7K7 TCGA-MI-A75G 
       13.38        14.24 

$`4P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
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-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        0.26        22.36        12.72         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-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-A1EK 
        6.71        12.95        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        73.38        14.07        14.24        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
      100.96        12.69        15.85        13.91         0.23         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       27.88         8.12         6.38         0.13         0.03         0.39 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       51.06        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.99         4.37         7.76         5.98         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
        4.01         2.14         0.49         9.57         5.10        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71         1.71        58.88        16.37         4.44 

  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 
           13.525            14.240 
[1] "0.1 - 79.7 (13.5)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1.3"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P LOSS MUTATED        10       13         0          5          1          1
  4P LOSS WILD-TYPE      55       24         2         26          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P LOSS MUTATED          1         1         1
  4P LOSS WILD-TYPE        0         0         1
D47V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 10                55
  STAGE II                13                24
  STAGE III                0                 2
  STAGE IIIA               5                26
  STAGE IIIB               1                 4
  STAGE IIIC               1                 4
  STAGE IV                 1                 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                T1 T2 T3 T4
  4P LOSS MUTATED   12 13  8  2
  4P LOSS WILD-TYPE 56 28 34  6
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              12                56
  T2              13                28
  T3               8                34
  T4               2                 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"
D47V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   16  2
  4P LOSS WILD-TYPE 86  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     16    2
  4P LOSS WILD-TYPE   86    1
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              16                86
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4P LOSS MUTATED   26  2  7
  4P LOSS WILD-TYPE 94  1 30
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              26                94
  M1               2                 1
  MX               7                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"
D47V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   12 23
  4P LOSS WILD-TYPE 48 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     12   23
  4P LOSS WILD-TYPE   48   77
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              12                48
  MALE                23                77
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4P LOSS MUTATED                         0                       34
  4P LOSS WILD-TYPE                       2                      122
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4P LOSS MUTATED                                  1
  4P LOSS WILD-TYPE                                1
D47V8, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      34               122
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED    29   3   1   2
  4P LOSS WILD-TYPE 102   8   0  10
D47V9, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              29               102
  R1               3                 8
  R2               1                 0
  RX               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0    10
  4P LOSS WILD-TYPE                                1    26
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           3    22
  4P LOSS WILD-TYPE                         5    87
D47V10, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10                26
  BLACK OR AFRICAN AMERICAN                      3                 5
  WHITE                                         22                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     0  32
  4P LOSS WILD-TYPE   3 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0   32
  4P LOSS WILD-TYPE    3  111
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              32               111
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   30 20
  4Q LOSS WILD-TYPE 61 46
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               50               107 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               20                46 
$`4Q LOSS MUTATED`
TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 
       27.52        23.34         5.03        13.84         0.26         9.50 
TCGA-BC-A69H TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
       14.60         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        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B TCGA-ED-A459 
       18.44        15.06        29.56        73.81         9.30        13.41 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A2KB 
       13.35         0.20         0.20         0.20         0.20        10.98 
TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y 
        0.62         8.12        60.36         1.22        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-KR-A7K7 
       21.53        14.70         4.37         1.84        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75G 
        0.49        14.24 

$`4Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KG 
        2.99        25.32         1.12        69.57        44.42        22.36 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       12.72         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
        3.32         0.07        83.57       113.00         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-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 
        6.71        12.95        18.35        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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        33.14        32.52        73.38        14.07 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       66.35        10.98         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
      100.96        12.69        15.85        13.91         0.23         0.20 
TCGA-ED-A82E 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-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       22.85        14.40        32.45        19.10        27.88         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        0.13         0.03         0.33         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        30.74        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 
       19.23        11.97         7.99         7.76         5.98         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
        2.66         4.01         2.14         9.57         5.10        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71         1.71        58.88        16.37         4.44 

  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 
           13.395            15.850 
[1] "0.1 - 79.7 (13.4)"  "0.0 - 113.0 (15.8)"
[1] "hr=" "1.3"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED        16       18         1          9          2          1
  4Q LOSS WILD-TYPE      49       19         1         22          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q LOSS MUTATED          1         1         1
  4Q LOSS WILD-TYPE        0         0         1
D48V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 16                49
  STAGE II                18                19
  STAGE III                1                 1
  STAGE IIIA               9                22
  STAGE IIIB               2                 3
  STAGE IIIC               1                 4
  STAGE IV                 1                 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                T1 T2 T3 T4
  4Q LOSS MUTATED   18 18 14  3
  4Q LOSS WILD-TYPE 50 23 28  5
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              18                50
  T2              18                23
  T3              14                28
  T4               3                 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"
D48V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   31  2
  4Q LOSS WILD-TYPE 71  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     31    2
  4Q LOSS WILD-TYPE   71    1
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              31                71
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4Q LOSS MUTATED   42  2  9
  4Q LOSS WILD-TYPE 78  1 28
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              42                78
  M1               2                 1
  MX               9                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"
D48V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   18 35
  4Q LOSS WILD-TYPE 42 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     18   35
  4Q LOSS WILD-TYPE   42   65
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              18                42
  MALE                35                65
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4Q LOSS MUTATED                         0                       52
  4Q LOSS WILD-TYPE                       2                      104
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4Q LOSS MUTATED                                  1
  4Q LOSS WILD-TYPE                                1
D48V8, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      52               104
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   46  4  1  2
  4Q LOSS WILD-TYPE 85  7  0 10
D48V9, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              46                85
  R1               4                 7
  R2               1                 0
  RX               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0    18
  4Q LOSS WILD-TYPE                                1    18
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           4    31
  4Q LOSS WILD-TYPE                         4    78
D48V10, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         18                18
  BLACK OR AFRICAN AMERICAN                      4                 4
  WHITE                                         31                78
[1] 4 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    1 48
  4Q LOSS WILD-TYPE  2 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   48
  4Q LOSS WILD-TYPE    2   95
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              48                95
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    6  5
  5P LOSS WILD-TYPE 85 61
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               146 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5                61 
$`5P LOSS MUTATED`
TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-A3M9 TCGA-DD-A11A TCGA-DD-A1EH TCGA-DD-A1EJ 
       46.78         0.07         0.10         2.60        49.15        29.16 
TCGA-DD-A4NB TCGA-ES-A2HS TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A7M9 
       32.52        22.85         0.33         1.22         1.84 

$`5P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
       12.72         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-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-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        45.11         6.02        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-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        33.14        73.38        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        0.13         0.03        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-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.99         4.37         7.76         5.98         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        5.10        14.24        12.85         8.71         1.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.07              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            49.15            113.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             2.60             13.99 
[1] "0.1 - 49.1 (2.6)"   "0.0 - 113.0 (14.0)"
[1] "hr=" "1.5"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P LOSS MUTATED         5        1         1          1          1          1
  5P LOSS WILD-TYPE      60       36         1         30          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P LOSS MUTATED          0         0         0
  5P LOSS WILD-TYPE        1         1         2
D49V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  5                60
  STAGE II                 1                36
  STAGE III                1                 1
  STAGE IIIA               1                30
  STAGE IIIB               1                 4
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    6  1  4  0
  5P LOSS WILD-TYPE 62 40 38  8
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               6                62
  T2               1                40
  T3               4                38
  T4               0                 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"
D49V5, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    6  1
  5P LOSS WILD-TYPE 96  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    1
  5P LOSS WILD-TYPE   96    2
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               6                96
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5P LOSS MUTATED     8   0   3
  5P LOSS WILD-TYPE 112   3  34
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               8               112
  M1               0                 3
  MX               3                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2  9
  5P LOSS WILD-TYPE 58 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    9
  5P LOSS WILD-TYPE   58   91
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               2                58
  MALE                 9                91
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5P LOSS MUTATED                         1                       10
  5P LOSS WILD-TYPE                       1                      146
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5P LOSS MUTATED                                  0
  5P LOSS WILD-TYPE                                2
D49V8, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      10               146
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED     9   1   0   1
  5P LOSS WILD-TYPE 122  10   1  11
D49V9, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               9               122
  R1               1                10
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     2
  5P LOSS WILD-TYPE                                1    34
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           1     8
  5P LOSS WILD-TYPE                         7   101
D49V10, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                34
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                          8               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  11
  5P LOSS WILD-TYPE   3 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   11
  5P LOSS WILD-TYPE    3  132
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              11               132
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    7  8
  5Q LOSS WILD-TYPE 84 58
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               15               142 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8                58 
$`5Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A10S TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A11A TCGA-DD-A1EF 
       10.13        46.78         4.24         0.10         2.60        12.95 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A4NB TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 
       49.15        29.16        32.52        22.85        27.88         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A7M9 
       60.36         1.22         1.84 

$`5Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        37.32        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA 
        0.07         2.86         0.39         3.39         3.32         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-A1EG 
       79.40        66.31        19.79        75.65         6.71        45.11 
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-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       19.10         8.12         6.38         0.13         0.03         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-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       14.70        11.97         7.99         4.37         7.76         5.98 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        1.71        58.88        16.37         4.44 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.10              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            60.36            113.00 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            12.95             13.99 
[1] "0.1 - 60.4 (12.9)"  "0.0 - 113.0 (14.0)"
[1] "hr=" "1.5"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED         6        1         1          3          1          1
  5Q LOSS WILD-TYPE      59       36         1         28          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q LOSS MUTATED          0         0         0
  5Q LOSS WILD-TYPE        1         1         2
D50V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  6                59
  STAGE II                 1                36
  STAGE III                1                 1
  STAGE IIIA               3                28
  STAGE IIIB               1                 4
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    7  1  7  0
  5Q LOSS WILD-TYPE 61 40 35  8
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               7                61
  T2               1                40
  T3               7                35
  T4               0                 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"
D50V5, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    7  1
  5Q LOSS WILD-TYPE 95  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    1
  5Q LOSS WILD-TYPE   95    2
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               7                95
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5Q LOSS MUTATED    11   0   4
  5Q LOSS WILD-TYPE 109   3  33
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              11               109
  M1               0                 3
  MX               4                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    5 10
  5Q LOSS WILD-TYPE 55 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5   10
  5Q LOSS WILD-TYPE   55   90
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               5                55
  MALE                10                90
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5Q LOSS MUTATED                         1                       13
  5Q LOSS WILD-TYPE                       1                      143
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5Q LOSS MUTATED                                  1
  5Q LOSS WILD-TYPE                                1
D50V8, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      13               143
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    12   2   0   1
  5Q LOSS WILD-TYPE 119   9   1  11
D50V9, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              12               119
  R1               2                 9
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     2
  5Q LOSS WILD-TYPE                                1    34
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           1    12
  5Q LOSS WILD-TYPE                         7    97
D50V10, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                34
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                         12                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"
D50V11, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0  15
  5Q LOSS WILD-TYPE   3 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   15
  5Q LOSS WILD-TYPE    3  128
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               128
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   10  7
  6P LOSS WILD-TYPE 81 59
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17               140 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                59 
$`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-ED-A66Y 
       18.35        19.76        14.24        39.78         0.23 

$`6P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        5.03        44.42        13.84         0.26        22.36        14.60 
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-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33         7.33         0.46        51.29        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       75.65        45.11        49.15        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       32.52        73.38        14.07        18.44        15.06        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-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         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        5.10        14.24        12.85         8.71         1.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.10              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           113.00            107.11 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           14.240            13.875 
[1] "0.1 - 113.0 (14.2)" "0.0 - 107.1 (13.9)"
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P LOSS MUTATED         7        2         0          5          1          1
  6P LOSS WILD-TYPE      58       35         2         26          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P LOSS MUTATED          0         0         1
  6P LOSS WILD-TYPE        1         1         1
D51V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  7                58
  STAGE II                 2                35
  STAGE III                0                 2
  STAGE IIIA               5                26
  STAGE IIIB               1                 4
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    8  2  6  1
  6P LOSS WILD-TYPE 60 39 36  7
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               8                60
  T2               2                39
  T3               6                36
  T4               1                 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"
D51V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   14  1
  6P LOSS WILD-TYPE 88  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     14    1
  6P LOSS WILD-TYPE   88    2
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              14                88
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6P LOSS MUTATED    16   1   0
  6P LOSS WILD-TYPE 104   2  37
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              16               104
  M1               1                 2
  MX               0                37
[1] 3 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    9  8
  6P LOSS WILD-TYPE 51 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9    8
  6P LOSS WILD-TYPE   51   92
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               9                51
  MALE                 8                92
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6P LOSS MUTATED                         0                       17
  6P LOSS WILD-TYPE                       2                      139
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6P LOSS MUTATED                                  0
  6P LOSS WILD-TYPE                                2
D51V8, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      17               139
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    15   1   0   1
  6P LOSS WILD-TYPE 116  10   1  11
D51V9, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              15               116
  R1               1                10
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     3
  6P LOSS WILD-TYPE                                1    33
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           1    12
  6P LOSS WILD-TYPE                         7    97
D51V10, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                33
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                         12                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"
D51V11, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0  15
  6P LOSS WILD-TYPE   3 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   15
  6P LOSS WILD-TYPE    3  128
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               128
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   28 19
  6Q LOSS WILD-TYPE 63 47
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               47               110 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19                47 
$`6Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-A3M9 
       37.32         0.26         9.50        12.72         2.86         0.10 
TCGA-CC-A3MA TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC 
        0.07       113.00         2.60        21.76        90.71        19.79 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
        6.71        12.95        45.11         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        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NS TCGA-DD-A73E TCGA-ED-A66Y TCGA-ED-A7PZ 
       15.06        39.78        80.75         1.45         0.23         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B 
        0.20         0.20        18.74        11.93        22.85        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T 
       19.10        27.88         6.38        60.36         1.22        51.06 
TCGA-G3-A25X TCGA-G3-A5SL TCGA-G3-A6UC TCGA-MI-A75E TCGA-MI-A75I 
       58.49         7.99         7.76         5.10         8.71 

$`6Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 
       44.42        13.84        22.36        14.60         0.07         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.39         4.24         3.32         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-A1EH TCGA-DD-A1EL TCGA-DD-A39V 
       79.40        66.31        75.65        49.15        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
        5.62        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
      107.11        13.78        30.61        32.52        73.38        14.07 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       18.44        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         0.20         0.20         0.20        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A3I1 TCGA-FV-A3R3 
       10.98         0.62         9.96        14.40         8.12         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.33         0.39        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-A7M9 
       19.23        14.70        11.97         4.37         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
        0.49         9.57        14.24        12.85         1.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           113.00            107.11 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            12.95             13.99 
[1] "0.1 - 113.0 (12.9)" "0.0 - 107.1 (14.0)"
[1] "hr=" "1"  
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED        17        8         0         13          2          4
  6Q LOSS WILD-TYPE      48       29         2         18          3          1
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q LOSS MUTATED          0         0         1
  6Q LOSS WILD-TYPE        1         1         1
D52V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 17                48
  STAGE II                 8                29
  STAGE III                0                 2
  STAGE IIIA              13                18
  STAGE IIIB               2                 3
  STAGE IIIC               4                 1
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED   18 11 15  3
  6Q LOSS WILD-TYPE 50 30 27  5
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              18                50
  T2              11                30
  T3              15                27
  T4               3                 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"
D52V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   31  2
  6Q LOSS WILD-TYPE 71  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     31    2
  6Q LOSS WILD-TYPE   71    1
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              31                71
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED   40  1  6
  6Q LOSS WILD-TYPE 80  2 31
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              40                80
  M1               1                 2
  MX               6                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   21 26
  6Q LOSS WILD-TYPE 39 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     21   26
  6Q LOSS WILD-TYPE   39   74
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              21                39
  MALE                26                74
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6Q LOSS MUTATED                         0                       46
  6Q LOSS WILD-TYPE                       2                      110
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6Q LOSS MUTATED                                  1
  6Q LOSS WILD-TYPE                                1
D52V8, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      46               110
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  6Q LOSS MUTATED   39  4  0  3
  6Q LOSS WILD-TYPE 92  7  1  9
D52V9, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              39                92
  R1               4                 7
  R2               0                 1
  RX               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     9
  6Q LOSS WILD-TYPE                                1    27
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           3    33
  6Q LOSS WILD-TYPE                         5    76
D52V10, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          9                27
  BLACK OR AFRICAN AMERICAN                      3                 5
  WHITE                                         33                76
[1] 4 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     0  43
  6Q LOSS WILD-TYPE   3 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   43
  6Q LOSS WILD-TYPE    3  100
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              43               100
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    3  5
  7P LOSS WILD-TYPE 88 61
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               149 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                61 
$`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-EP-A2KB TCGA-FV-A3I1 
       10.98         8.12 

$`7P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
        5.03        44.42         0.26         9.50        14.60        12.72 
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-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-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-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        73.38        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       22.85        14.40        32.45        19.10        27.88         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-A7M7 
       14.70        11.97         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71         1.71        58.88        16.37         4.44 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.10              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            55.69            113.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           11.965            14.240 
[1] "0.1 - 55.7 (12.0)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "2.3"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P LOSS MUTATED         3        4         0          1          0          0
  7P LOSS WILD-TYPE      62       33         2         30          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P LOSS MUTATED          0         0         0
  7P LOSS WILD-TYPE        1         1         2
D53V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  3                62
  STAGE II                 4                33
  STAGE III                0                 2
  STAGE IIIA               1                30
  STAGE IIIB               0                 5
  STAGE IIIC               0                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7P LOSS MUTATED    3  4  1  0
  7P LOSS WILD-TYPE 65 37 41  8
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               3                65
  T2               4                37
  T3               1                41
  T4               0                 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"
D53V5, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    5  0
  7P LOSS WILD-TYPE 97  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5    0
  7P LOSS WILD-TYPE   97    3
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               5                97
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7P LOSS MUTATED     6   0   2
  7P LOSS WILD-TYPE 114   3  35
D53V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               6               114
  M1               0                 3
  MX               2                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    6  2
  7P LOSS WILD-TYPE 54 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      6    2
  7P LOSS WILD-TYPE   54   98
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               6                54
  MALE                 2                98
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7P LOSS MUTATED                         0                        8
  7P LOSS WILD-TYPE                       2                      148
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7P LOSS MUTATED                                  0
  7P LOSS WILD-TYPE                                2
D53V8, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                       8               148
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED     7   0   0   1
  7P LOSS WILD-TYPE 124  11   1  11
D53V9, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0               7               124
  R1               0                11
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     2
  7P LOSS WILD-TYPE                                1    34
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           0     6
  7P LOSS WILD-TYPE                         8   103
D53V10, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                34
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          6               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   7
  7P LOSS WILD-TYPE   3 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    7
  7P LOSS WILD-TYPE    3  136
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               7               136
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    4  7
  7Q LOSS WILD-TYPE 87 59
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               146 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7                59 
$`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-A4ND TCGA-ED-A7PX TCGA-EP-A2KB TCGA-G3-A25S 
       55.69        73.38         0.20        10.98         1.22 

$`7Q LOSS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       44.42         0.26         9.50        14.60        12.72         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-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-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-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33        60.36         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-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         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        5.10        14.24        12.85         8.71         1.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.20              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            73.38            113.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           13.640            14.155 
[1] "0.2 - 73.4 (13.6)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1.7"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q LOSS MUTATED         5        5         0          1          0          0
  7Q LOSS WILD-TYPE      60       32         2         30          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q LOSS MUTATED          0         0         0
  7Q LOSS WILD-TYPE        1         1         2
D54V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  5                60
  STAGE II                 5                32
  STAGE III                0                 2
  STAGE IIIA               1                30
  STAGE IIIB               0                 5
  STAGE IIIC               0                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7Q LOSS MUTATED    5  5  1  0
  7Q LOSS WILD-TYPE 63 36 41  8
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               5                63
  T2               5                36
  T3               1                41
  T4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V5, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    7  0
  7Q LOSS WILD-TYPE 95  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      7    0
  7Q LOSS WILD-TYPE   95    3
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               7                95
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7Q LOSS MUTATED    10   0   1
  7Q LOSS WILD-TYPE 110   3  36
D54V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0              10               110
  M1               0                 3
  MX               1                36
[1] 3 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    8  3
  7Q LOSS WILD-TYPE 52 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      8    3
  7Q LOSS WILD-TYPE   52   97
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               8                52
  MALE                 3                97
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7Q LOSS MUTATED                         0                       11
  7Q LOSS WILD-TYPE                       2                      145
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7Q LOSS MUTATED                                  0
  7Q LOSS WILD-TYPE                                2
D54V8, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      11               145
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED     8   2   0   1
  7Q LOSS WILD-TYPE 123   9   1  11
D54V9, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               8               123
  R1               2                 9
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     2
  7Q LOSS WILD-TYPE                                1    34
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           1     8
  7Q LOSS WILD-TYPE                         7   101
D54V10, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                34
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                          8               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  10
  7Q LOSS WILD-TYPE   3 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   10
  7Q LOSS WILD-TYPE    3  133
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              10               133
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   41 34
  8P LOSS WILD-TYPE 50 32
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               75                82 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               34                32 
$`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-CC-5261 
       13.84         0.26        22.36        14.60        12.72         0.39 
TCGA-CC-5262 TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11C 
        3.39        79.73        83.57        53.33       113.00        21.76 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y 
        6.71        45.11        29.16        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-A4NA TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        73.38        14.24        18.44        15.06        39.78 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-EP-A12J 
        1.45        27.72       100.96         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        11.74         0.62        11.93        22.85        14.40 
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-A5SJ 
        1.22        28.27        30.74        22.13        19.53        11.97 
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75E 
        7.76         1.84         2.66         4.01         9.57         5.10 
TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
        8.71        16.37         4.44 

$`8P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        27.91        46.78         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 
        1.12        69.57         9.50         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-A39X TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       18.35        55.69         7.66        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
      107.11        32.52        14.07        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       93.67        12.26        80.75        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A496 
        0.20        10.98         9.96        32.45         0.13         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39        51.06        53.79        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM 
       25.64         5.92        19.23        14.70         7.99         4.37 
TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        5.98         1.02         2.14        11.84        13.38         0.49 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
       14.24        12.85         1.71        58.88 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.03              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           113.00            107.11 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           14.400            13.395 
[1] "0.0 - 113.0 (14.4)" "0.1 - 107.1 (13.4)"
[1] "hr=" "1.3"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P LOSS MUTATED        30       19         0         10          5          4
  8P LOSS WILD-TYPE      35       18         2         21          0          1
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P LOSS MUTATED          0         1         1
  8P LOSS WILD-TYPE        1         0         1
D55V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 30                35
  STAGE II                19                18
  STAGE III                0                 2
  STAGE IIIA              10                21
  STAGE IIIB               5                 0
  STAGE IIIC               4                 1
  STAGE IV                 0                 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                T1 T2 T3 T4
  8P LOSS MUTATED   32 23 17  4
  8P LOSS WILD-TYPE 36 18 25  4
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              32                36
  T2              23                18
  T3              17                25
  T4               4                 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"
D55V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   40  3
  8P LOSS WILD-TYPE 62  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     40    3
  8P LOSS WILD-TYPE   62    0
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              40                62
  1               3                 0
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED   54  1 21
  8P LOSS WILD-TYPE 66  2 16
D55V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              54                66
  M1               1                 2
  MX              21                16
[1] 3 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   28 48
  8P LOSS WILD-TYPE 32 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     28   48
  8P LOSS WILD-TYPE   32   52
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              28                32
  MALE                48                52
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8P LOSS MUTATED                         0                       75
  8P LOSS WILD-TYPE                       2                       81
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8P LOSS MUTATED                                  1
  8P LOSS WILD-TYPE                                1
D55V8, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      75                81
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   62  7  0  4
  8P LOSS WILD-TYPE 69  4  1  8
D55V9, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              62                69
  R1               7                 4
  R2               0                 1
  RX               4                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1     7
  8P LOSS WILD-TYPE                                0    29
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           5    59
  8P LOSS WILD-TYPE                         3    50
D55V10, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          7                29
  BLACK OR AFRICAN AMERICAN                      5                 3
  WHITE                                         59                50
[1] 4 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    2 66
  8P LOSS WILD-TYPE  1 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2   66
  8P LOSS WILD-TYPE    1   77
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO              66                77
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    8  8
  8Q LOSS WILD-TYPE 83 58
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               16               141 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8                58 
$`8Q LOSS MUTATED`
TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-DD-A115 TCGA-DD-A3A0 
       27.52        13.84        22.36         0.39        83.57        25.81 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NK TCGA-DD-A73C TCGA-ED-A7PY TCGA-EP-A2KA 
       30.61        33.14        39.78         7.56         0.20        11.74 
TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A7M9 TCGA-NI-A8LF 
       27.88         0.03         1.84        16.37 

$`8Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       44.42         0.26         9.50        14.60        12.72         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        79.73        37.78        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-A3A1 TCGA-DD-A3A2 
       21.14        55.69         5.62        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        14.07        14.24        18.44        15.06 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E 
       80.75        66.35        10.98         9.30        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-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-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38         0.13         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-A7M7 
       14.70        11.97         7.99         4.37         7.76         5.98 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
        1.71        58.88         4.44 

  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 
           19.365            13.780 
[1] "0.0 - 83.6 (19.4)"  "0.1 - 113.0 (13.8)"
[1] "hr=" "1.3"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q LOSS MUTATED         2        6         0          4          1          1
  8Q LOSS WILD-TYPE      63       31         2         27          4          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q LOSS MUTATED          0         0         1
  8Q LOSS WILD-TYPE        1         1         1
D56V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  2                63
  STAGE II                 6                31
  STAGE III                0                 2
  STAGE IIIA               4                27
  STAGE IIIB               1                 4
  STAGE IIIC               1                 4
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8Q LOSS MUTATED    2  7  5  2
  8Q LOSS WILD-TYPE 66 34 37  6
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               2                66
  T2               7                34
  T3               5                37
  T4               2                 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"
D56V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    6  1
  8Q LOSS WILD-TYPE 96  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6    1
  8Q LOSS WILD-TYPE   96    2
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               6                96
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8Q LOSS MUTATED    11   1   4
  8Q LOSS WILD-TYPE 109   2  33
D56V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0              11               109
  M1               1                 2
  MX               4                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED   10  6
  8Q LOSS WILD-TYPE 50 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10    6
  8Q LOSS WILD-TYPE   50   94
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              10                50
  MALE                 6                94
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8Q LOSS MUTATED                         0                       15
  8Q LOSS WILD-TYPE                       2                      141
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8Q LOSS MUTATED                                  1
  8Q LOSS WILD-TYPE                                1
D56V8, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      15               141
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    14   1   0   1
  8Q LOSS WILD-TYPE 117  10   1  11
D56V9, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              14               117
  R1               1                10
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     2
  8Q LOSS WILD-TYPE                                1    34
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           0    14
  8Q LOSS WILD-TYPE                         8    95
D56V10, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                34
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                         14                95
[1] 4 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  14
  8Q LOSS WILD-TYPE   3 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   14
  8Q LOSS WILD-TYPE    3  129
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              14               129
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   23 23
  9P LOSS WILD-TYPE 68 43
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               46               111 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               23                43 
$`9P LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A112 
       48.99        37.32        10.13        46.78        27.52         5.03 
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT 
       13.84         9.50        14.60         0.07         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.10         0.13        79.73        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG 
        7.33         2.60         0.46        21.76        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
        6.02        29.16        18.35        55.69         5.62        25.81 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NO TCGA-ED-A459 TCGA-ED-A66X 
       30.61        73.38        18.44        73.81        13.41        13.35 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A3I1 TCGA-G3-A25S 
        0.20         0.20         0.62        11.93         8.12         1.22 
TCGA-G3-A25T TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF 
       51.06        14.24         8.71        16.37 

$`9P LOSS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.91        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-CC-5260 
       69.57        44.42         0.26        22.36        12.72         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        14.07        14.24        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       27.72       100.96        12.69        15.85        13.91         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-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         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       11.84        13.38         0.49         9.57         5.10        12.85 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
        1.71        58.88         4.44 

  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 
            13.38             14.24 
[1] "0.1 - 83.6 (13.4)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1.5"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P LOSS MUTATED        15       10         0         12          0          1
  9P LOSS WILD-TYPE      50       27         2         19          5          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P LOSS MUTATED          1         1         2
  9P LOSS WILD-TYPE        0         0         0
D57V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 15                50
  STAGE II                10                27
  STAGE III                0                 2
  STAGE IIIA              12                19
  STAGE IIIB               0                 5
  STAGE IIIC               1                 4
  STAGE IV                 1                 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                T1 T2 T3 T4
  9P LOSS MUTATED   17 13 16  2
  9P LOSS WILD-TYPE 51 28 26  6
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              17                51
  T2              13                28
  T3              16                26
  T4               2                 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"
D57V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   28  2
  9P LOSS WILD-TYPE 74  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     28    2
  9P LOSS WILD-TYPE   74    1
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              28                74
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED   33  3 12
  9P LOSS WILD-TYPE 87  0 25
D57V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              33                87
  M1               3                 0
  MX              12                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   14 34
  9P LOSS WILD-TYPE 46 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     14   34
  9P LOSS WILD-TYPE   46   66
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              14                46
  MALE                34                66
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9P LOSS MUTATED                         0                       48
  9P LOSS WILD-TYPE                       2                      108
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9P LOSS MUTATED                                  0
  9P LOSS WILD-TYPE                                2
D57V8, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      48               108
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED   35  5  1  5
  9P LOSS WILD-TYPE 96  6  0  7
D57V9, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              35                96
  R1               5                 6
  R2               1                 0
  RX               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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0    14
  9P LOSS WILD-TYPE                                1    22
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           3    31
  9P LOSS WILD-TYPE                         5    78
D57V10, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                22
  BLACK OR AFRICAN AMERICAN                      3                 5
  WHITE                                         31                78
[1] 4 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    0 46
  9P LOSS WILD-TYPE  3 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   46
  9P LOSS WILD-TYPE    3   97
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              46                97
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   26 22
  9Q LOSS WILD-TYPE 65 44
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               48               109 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22                44 
$`9Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A217 
       37.32        10.13        46.78        27.52         5.03        13.84 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT 
        9.50        14.60         0.07         2.86         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 
        0.10         0.10         0.13        79.73        53.33         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI 
        2.60         0.46        21.76        12.95        45.11         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NA 
       29.16        18.35        55.69         5.62        30.61        33.14 
TCGA-DD-A4NI TCGA-DD-A4NO TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP 
       18.44        73.81        13.41        13.35         0.20         0.20 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
        0.62        11.93        27.88         8.12         6.38         0.13 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CH TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF 
        1.22        51.06        25.64        14.24         8.71        16.37 

$`9Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        27.91        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-A69I 
        1.12        69.57        44.42         0.26        22.36        12.72 
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        14.07        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.78        56.25        29.56        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         1.45        27.72       100.96        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 
       13.91         0.23         0.20         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-A7M7 TCGA-G3-A7M9 
       11.97         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
        0.49         9.57         5.10        12.85         1.71        58.88 
TCGA-O8-A75V 
        4.44 

  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 
            12.44             14.70 
[1] "0.1 - 79.7 (12.4)"  "0.0 - 113.0 (14.7)"
[1] "hr=" "1.7"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED        15       11         0         11          0          3
  9Q LOSS WILD-TYPE      50       26         2         20          5          2
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q LOSS MUTATED          1         1         2
  9Q LOSS WILD-TYPE        0         0         0
D58V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 15                50
  STAGE II                11                26
  STAGE III                0                 2
  STAGE IIIA              11                20
  STAGE IIIB               0                 5
  STAGE IIIC               3                 2
  STAGE IV                 1                 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                T1 T2 T3 T4
  9Q LOSS MUTATED   17 15 15  3
  9Q LOSS WILD-TYPE 51 26 27  5
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              17                51
  T2              15                26
  T3              15                27
  T4               3                 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"
D58V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   27  3
  9Q LOSS WILD-TYPE 75  0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     27    3
  9Q LOSS WILD-TYPE   75    0
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              27                75
  1               3                 0
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED   33  3 14
  9Q LOSS WILD-TYPE 87  0 23
D58V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              33                87
  M1               3                 0
  MX              14                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   16 34
  9Q LOSS WILD-TYPE 44 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     16   34
  9Q LOSS WILD-TYPE   44   66
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              16                44
  MALE                34                66
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9Q LOSS MUTATED                         0                       49
  9Q LOSS WILD-TYPE                       2                      107
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9Q LOSS MUTATED                                  1
  9Q LOSS WILD-TYPE                                1
D58V8, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      49               107
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED   37  4  1  6
  9Q LOSS WILD-TYPE 94  7  0  6
D58V9, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              37                94
  R1               4                 7
  R2               1                 0
  RX               6                 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
  9Q LOSS MUTATED                                  0    16
  9Q LOSS WILD-TYPE                                1    20
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           3    31
  9Q LOSS WILD-TYPE                         5    78
D58V10, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         16                20
  BLACK OR AFRICAN AMERICAN                      3                 5
  WHITE                                         31                78
[1] 4 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    0 49
  9Q LOSS WILD-TYPE  3 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0   49
  9Q LOSS WILD-TYPE    3   94
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              49                94
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   14  4
  10P LOSS WILD-TYPE 77 62
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                18                139 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 62 
$`10P LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-CC-A3M9 TCGA-CC-A3MA 
       27.91         5.03        13.84         9.50         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NQ 
        0.13         2.60        21.76         5.62        18.44        12.26 
TCGA-ED-A7PX TCGA-FV-A3I0 TCGA-G3-A25X TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-NI-A4U2 
        0.20        27.88        58.49        11.84        13.38        58.88 

$`10P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
        0.26        22.36        14.60        12.72         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-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-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-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.07        14.24        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       73.81        93.67         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-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-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-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-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
       11.97         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C 
        1.02         2.66         4.01         2.14         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF 
        5.10        14.24        12.85         8.71         1.71        16.37 
TCGA-O8-A75V 
        4.44 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             58.88             113.00 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             12.05              14.24 
[1] "0.1 - 58.9 (12.1)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1.3"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10P LOSS MUTATED         5        7         0          6          0
  10P LOSS WILD-TYPE      60       30         2         25          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P LOSS MUTATED            0        0         1         0
  10P LOSS WILD-TYPE          5        1         0         2
D59V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   5                 60
  STAGE II                  7                 30
  STAGE III                 0                  2
  STAGE IIIA                6                 25
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  0                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    6  7  7  0
  10P LOSS WILD-TYPE 62 34 35  8
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                6                 62
  T2                7                 34
  T3                7                 35
  T4                0                  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"
D59V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   10  1
  10P LOSS WILD-TYPE 92  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     10    1
  10P LOSS WILD-TYPE   92    2
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               10                 92
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10P LOSS MUTATED    15   0   5
  10P LOSS WILD-TYPE 105   3  32
D59V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               15                105
  M1                0                  3
  MX                5                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    4 16
  10P LOSS WILD-TYPE 56 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4   16
  10P LOSS WILD-TYPE   56   84
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                4                 56
  MALE                 16                 84
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10P LOSS MUTATED                         0                       18
  10P LOSS WILD-TYPE                       2                      138
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10P LOSS MUTATED                                  2
  10P LOSS WILD-TYPE                                0
D59V8, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       18                138
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    16   2   0   2
  10P LOSS WILD-TYPE 115   9   1  10
D59V9, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               16                115
  R1                2                  9
  R2                0                  1
  RX                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     6
  10P LOSS WILD-TYPE                                1    30
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           1    13
  10P LOSS WILD-TYPE                         7    96
D59V10, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 30
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                          13                 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"
D59V11, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  16
  10P LOSS WILD-TYPE   2 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   16
  10P LOSS WILD-TYPE    2  127
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               16                127
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   19 12
  10Q LOSS WILD-TYPE 72 54
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                31                126 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                12                 54 
$`10Q LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 
       27.91        37.32        10.13         2.99         5.03        13.84 
TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        9.50         2.86         3.32         0.10         0.07         0.13 
TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y 
       37.78         2.60        21.76        45.11        13.64         5.62 
TCGA-DD-A4NI TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A7PX TCGA-FV-A3I0 TCGA-FV-A496 
       18.44        12.26        13.41         0.20        27.88         0.33 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A5SJ TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MR-A8JO 
       53.79        58.49        11.97        11.84        13.38         1.71 
TCGA-NI-A4U2 
       58.88 

$`10Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        46.78        27.52        27.52        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-A69I TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MB 
       12.72         0.07         0.39         3.39         4.24         0.10 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       79.73        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
        6.71        12.95        49.15         6.02        29.16        18.35 
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-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        14.07        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         1.45        27.72       100.96        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       19.10         8.12         6.38         0.13         0.03        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39         1.22        51.06        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
       14.70         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C 
        1.02         2.66         4.01         2.14         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        16.37         4.44 

  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 
             11.97              14.65 
[1] "0.1 - 58.9 (12.0)"  "0.0 - 113.0 (14.6)"
[1] "hr=" "1.3"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED        10       10         0          8          0
  10Q LOSS WILD-TYPE      55       27         2         23          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q LOSS MUTATED            1        0         1         0
  10Q LOSS WILD-TYPE          4        1         0         2
D60V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  10                 55
  STAGE II                 10                 27
  STAGE III                 0                  2
  STAGE IIIA                8                 23
  STAGE IIIB                0                  5
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED   11 11 10  2
  10Q LOSS WILD-TYPE 57 30 32  6
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               11                 57
  T2               11                 30
  T3               10                 32
  T4                2                  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"
D60V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   18  1
  10Q LOSS WILD-TYPE 84  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     18    1
  10Q LOSS WILD-TYPE   84    2
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               18                 84
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED   25  0  9
  10Q LOSS WILD-TYPE 95  3 28
D60V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               25                 95
  M1                0                  3
  MX                9                 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"
D60V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    9 25
  10Q LOSS WILD-TYPE 51 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      9   25
  10Q LOSS WILD-TYPE   51   75
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                9                 51
  MALE                 25                 75
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10Q LOSS MUTATED                         1                       31
  10Q LOSS WILD-TYPE                       1                      125
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10Q LOSS MUTATED                                  2
  10Q LOSS WILD-TYPE                                0
D60V8, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       31                125
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    24   4   0   5
  10Q LOSS WILD-TYPE 107   7   1   7
D60V9, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               24                107
  R1                4                  7
  R2                0                  1
  RX                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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0    12
  10Q LOSS WILD-TYPE                                1    24
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           3    19
  10Q LOSS WILD-TYPE                         5    90
D60V10, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                 24
  BLACK OR AFRICAN AMERICAN                       3                  5
  WHITE                                          19                 90
[1] 4 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  29
  10Q LOSS WILD-TYPE   2 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   29
  10Q LOSS WILD-TYPE    2  114
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               29                114
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   14 11
  11P LOSS WILD-TYPE 77 55
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                25                132 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                11                 55 
$`11P LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-A3MA TCGA-CC-A3MC 
       37.32        46.78         5.03        13.84         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X 
       79.73        83.57        90.71        12.95        29.16        55.69 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NI TCGA-ED-A7PZ TCGA-EP-A2KC TCGA-FV-A496 
       32.52        73.38        18.44         0.20         0.62         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-KR-A7K7 
       60.36         1.22        11.97         1.84        11.84        13.38 
TCGA-MI-A75G 
       14.24 

$`11P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF 
       25.32        23.34         1.12        69.57        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       22.36         9.50        14.60        12.72         0.07         2.86 
TCGA-CC-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-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        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-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
        6.71        45.11        49.15         6.02        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.61        33.14        14.07        14.24        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 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-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       27.88         8.12         6.38         0.13         0.03         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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 
       14.70         7.99         4.37         7.76         5.98         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.66         4.01         2.14         0.49         9.57         5.10 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         8.71         1.71        58.88        16.37         4.44 

  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 
             13.84              13.99 
[1] "0.1 - 90.7 (13.8)"  "0.0 - 113.0 (14.0)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P LOSS MUTATED        10        6         0          5          1
  11P LOSS WILD-TYPE      55       31         2         26          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P LOSS MUTATED            1        0         1         0
  11P LOSS WILD-TYPE          4        1         0         2
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  10                 55
  STAGE II                  6                 31
  STAGE III                 0                  2
  STAGE IIIA                5                 26
  STAGE IIIB                1                  4
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED   12  7  8  0
  11P LOSS WILD-TYPE 56 34 34  8
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               12                 56
  T2                7                 34
  T3                8                 34
  T4                0                  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"
D61V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   13  2
  11P LOSS WILD-TYPE 89  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13    2
  11P LOSS WILD-TYPE   89    1
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               13                 89
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED   21  0  6
  11P LOSS WILD-TYPE 99  3 31
D61V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               21                 99
  M1                0                  3
  MX                6                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    9 18
  11P LOSS WILD-TYPE 51 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      9   18
  11P LOSS WILD-TYPE   51   82
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                9                 51
  MALE                 18                 82
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11P LOSS MUTATED                         1                       25
  11P LOSS WILD-TYPE                       1                      131
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11P LOSS MUTATED                                  1
  11P LOSS WILD-TYPE                                1
D61V8, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       25                131
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    23   3   0   1
  11P LOSS WILD-TYPE 108   8   1  11
D61V9, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               23                108
  R1                3                  8
  R2                0                  1
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     4
  11P LOSS WILD-TYPE                                1    32
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           1    22
  11P LOSS WILD-TYPE                         7    87
D61V10, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                 32
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                          22                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  23
  11P LOSS WILD-TYPE   3 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   23
  11P LOSS WILD-TYPE    3  120
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               23                120
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   14 12
  11Q LOSS WILD-TYPE 77 54
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                26                131 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                12                 54 
$`11Q LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-5263 
       27.91        37.32        46.78         5.03        13.84         4.24 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EF 
        0.13        79.73        83.57         2.60        90.71        12.95 
TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A73B 
       29.16        55.69        32.52        73.38        18.44         9.30 
TCGA-ED-A7PZ TCGA-EP-A2KC TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ 
        0.20         0.62         0.33        60.36         1.22        11.97 
TCGA-KR-A7K2 TCGA-KR-A7K7 
       11.84        13.38 

$`11Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        10.13        27.52        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-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        9.50        14.60        12.72         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-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-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-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y 
       49.15         6.02        18.35        13.64        21.14         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-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.07        14.24        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-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-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-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        11.74        10.98         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-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-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-A5SL TCGA-G3-A5SM 
        5.92        19.53        19.23        14.70         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        2.14         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71         1.71        58.88        16.37         4.44 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.13               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             90.71             113.00 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             13.61              14.07 
[1] "0.1 - 90.7 (13.6)"  "0.0 - 113.0 (14.1)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11Q LOSS MUTATED        12        5         0          6          0
  11Q LOSS WILD-TYPE      53       32         2         25          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q LOSS MUTATED            1        0         1         0
  11Q LOSS WILD-TYPE          4        1         0         2
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  12                 53
  STAGE II                  5                 32
  STAGE III                 0                  2
  STAGE IIIA                6                 25
  STAGE IIIB                0                  5
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED   14  6  8  0
  11Q LOSS WILD-TYPE 54 35 34  8
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               14                 54
  T2                6                 35
  T3                8                 34
  T4                0                  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"
D62V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   15  2
  11Q LOSS WILD-TYPE 87  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     15    2
  11Q LOSS WILD-TYPE   87    1
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               15                 87
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED   22  0  6
  11Q LOSS WILD-TYPE 98  3 31
D62V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               22                 98
  M1                0                  3
  MX                6                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   10 18
  11Q LOSS WILD-TYPE 50 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     10   18
  11Q LOSS WILD-TYPE   50   82
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               10                 50
  MALE                 18                 82
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11Q LOSS MUTATED                         1                       26
  11Q LOSS WILD-TYPE                       1                      130
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11Q LOSS MUTATED                                  1
  11Q LOSS WILD-TYPE                                1
D62V8, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       26                130
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    22   4   0   2
  11Q LOSS WILD-TYPE 109   7   1  10
D62V9, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               22                109
  R1                4                  7
  R2                0                  1
  RX                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     4
  11Q LOSS WILD-TYPE                                1    32
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           2    22
  11Q LOSS WILD-TYPE                         6    87
D62V10, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                 32
  BLACK OR AFRICAN AMERICAN                       2                  6
  WHITE                                          22                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  23
  11Q LOSS WILD-TYPE   2 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   23
  11Q LOSS WILD-TYPE    2  120
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               23                120
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED   15 12
  12P LOSS WILD-TYPE 76 54
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                27                130 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                 54 
$`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        14.24        18.44        15.06        73.81        27.72 
TCGA-ED-A7XP TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A496 TCGA-G3-A25S 
        0.20         0.62         8.12         6.38         0.33         1.22 
TCGA-G3-A25Z TCGA-MI-A75G TCGA-MI-A75I 
       21.53        14.24         8.71 

$`12P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
        5.03        44.42         0.26        22.36        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 
        0.07         2.86         0.39         3.39         4.24         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.10        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         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-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
        6.02        18.35        21.14        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL 
       30.61        32.52        73.38        14.07        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G 
       10.98         9.30         7.56        10.98         1.45       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        11.74        10.98         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        32.45        19.10        27.88         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-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         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       11.84        13.38         0.49         9.57         5.10        12.85 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        1.71        58.88        16.37         4.44 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.13               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             73.81             113.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            13.640             14.235 
[1] "0.1 - 73.8 (13.6)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1.4"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED        10        7         1          4          1
  12P LOSS WILD-TYPE      55       30         1         27          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P LOSS MUTATED            2        1         0         0
  12P LOSS WILD-TYPE          3        0         1         2
D63V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  10                 55
  STAGE II                  7                 30
  STAGE III                 1                  1
  STAGE IIIA                4                 27
  STAGE IIIB                1                  4
  STAGE IIIC                2                  3
  STAGE IV                  1                  0
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED   11  9  7  0
  12P LOSS WILD-TYPE 57 32 35  8
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               11                 57
  T2                9                 32
  T3                7                 35
  T4                0                  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"
D63V5, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   16  2
  12P LOSS WILD-TYPE 86  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     16    2
  12P LOSS WILD-TYPE   86    1
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               16                 86
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12P LOSS MUTATED   22  1  4
  12P LOSS WILD-TYPE 98  2 33
D63V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0               22                 98
  M1                1                  2
  MX                4                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   10 17
  12P LOSS WILD-TYPE 50 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     10   17
  12P LOSS WILD-TYPE   50   83
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               10                 50
  MALE                 17                 83
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12P LOSS MUTATED                         0                       27
  12P LOSS WILD-TYPE                       2                      129
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12P LOSS MUTATED                                  0
  12P LOSS WILD-TYPE                                2
D63V8, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       27                129
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    23   2   1   0
  12P LOSS WILD-TYPE 108   9   0  12
D63V9, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               23                108
  R1                2                  9
  R2                1                  0
  RX                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     6
  12P LOSS WILD-TYPE                                1    30
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           3    17
  12P LOSS WILD-TYPE                         5    92
D63V10, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 30
  BLACK OR AFRICAN AMERICAN                       3                  5
  WHITE                                          17                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  25
  12P LOSS WILD-TYPE   3 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   25
  12P LOSS WILD-TYPE    3  118
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               25                118
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    8  8
  12Q LOSS WILD-TYPE 83 58
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                16                141 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                 58 
$`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-EP-A2KC 
       13.64        55.69         5.62        18.44        73.81         0.62 
TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A25Z TCGA-MI-A75G 
        8.12         0.33        21.53        14.24 

$`12Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        44.42         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       12.72         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.10         0.07         0.10        79.73        37.78        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-A39V TCGA-DD-A39Z 
       12.95         6.02        29.16        18.35        21.14        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        14.07        14.24        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
        0.23         0.20         0.20         0.20         0.20         0.20 
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-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
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-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         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        0.49         9.57         5.10        12.85         8.71         1.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  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 
             13.74              14.07 
[1] "0.1 - 73.8 (13.7)"  "0.0 - 113.0 (14.1)"
[1] "hr=" "1.4"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED         7        5         1          2          0
  12Q LOSS WILD-TYPE      58       32         1         29          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q LOSS MUTATED            0        1         0         0
  12Q LOSS WILD-TYPE          5        0         1         2
D64V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   7                 58
  STAGE II                  5                 32
  STAGE III                 1                  1
  STAGE IIIA                2                 29
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  1                  0
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12Q LOSS MUTATED    7  5  4  0
  12Q LOSS WILD-TYPE 61 36 38  8
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                7                 61
  T2                5                 36
  T3                4                 38
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V5, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   10  0
  12Q LOSS WILD-TYPE 92  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     10    0
  12Q LOSS WILD-TYPE   92    3
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               10                 92
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12Q LOSS MUTATED    13   1   2
  12Q LOSS WILD-TYPE 107   2  35
D64V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0               13                107
  M1                1                  2
  MX                2                 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"
D64V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    4 12
  12Q LOSS WILD-TYPE 56 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4   12
  12Q LOSS WILD-TYPE   56   88
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                4                 56
  MALE                 12                 88
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12Q LOSS MUTATED                         0                       16
  12Q LOSS WILD-TYPE                       2                      140
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12Q LOSS MUTATED                                  0
  12Q LOSS WILD-TYPE                                2
D64V8, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       16                140
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    14   0   1   0
  12Q LOSS WILD-TYPE 117  11   0  12
D64V9, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               14                117
  R1                0                 11
  R2                1                  0
  RX                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     5
  12Q LOSS WILD-TYPE                                1    31
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           2     9
  12Q LOSS WILD-TYPE                         6   100
D64V10, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 31
  BLACK OR AFRICAN AMERICAN                       2                  6
  WHITE                                           9                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  15
  12Q LOSS WILD-TYPE   3 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   15
  12Q LOSS WILD-TYPE    3  128
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               15                128
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   33 21
  13Q LOSS WILD-TYPE 58 45
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                54                103 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                21                 45 
$`13Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 
       37.32        10.13        27.52         2.99         5.03        13.84 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       22.36         9.50        14.60         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        3.39         0.10         0.07        79.73        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK 
      113.00         2.60        21.76        12.95         6.02        18.35 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NA 
       55.69         5.62        25.81       102.74        30.61        33.14 
TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-A73G 
       14.24        29.56        73.81        12.26        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A3RK 
       13.41        12.69         0.20         0.20         0.20        11.93 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CH 
       27.88         6.38         1.22        51.06        58.49        25.64 
TCGA-G3-A5SM TCGA-KR-A7K2 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF 
        4.37        11.84        14.24         8.71         1.71        16.37 

$`13Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        27.91        46.78        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69I TCGA-CC-5263 
        1.12        69.57        44.42         0.26        12.72         4.24 
TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11B 
        3.32         0.10         0.13        37.78         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
        6.71        45.11        49.15        29.16        13.64        21.14 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       19.76         7.66        70.06        17.59        20.12       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI 
       13.78         0.36        32.52        73.38        14.07        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       15.06        39.78        56.25        93.67         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A8O5 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-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 
        9.96        22.85        14.40        32.45        19.10         8.12 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U 
        0.13         0.03         0.33        60.36         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       28.27        30.74        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-A6UC 
       19.53        19.23        14.70        11.97         7.99         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-NI-A4U2 
       13.38         0.49         9.57         5.10        12.85        58.88 
TCGA-O8-A75V 
        4.44 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            113.00             107.11 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            13.625             14.070 
[1] "0.1 - 113.0 (13.6)" "0.0 - 107.1 (14.1)"
[1] "hr=" "1.2"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED        17       17         1          9          1
  13Q LOSS WILD-TYPE      48       20         1         22          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q LOSS MUTATED            3        0         0         2
  13Q LOSS WILD-TYPE          2        1         1         0
D65V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  17                 48
  STAGE II                 17                 20
  STAGE III                 1                  1
  STAGE IIIA                9                 22
  STAGE IIIB                1                  4
  STAGE IIIC                3                  2
  STAGE IV                  0                  1
  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                 T1 T2 T3 T4
  13Q LOSS MUTATED   17 20 13  6
  13Q LOSS WILD-TYPE 51 21 29  2
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               17                 51
  T2               20                 21
  T3               13                 29
  T4                6                  2
[1] 4 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   35  1
  13Q LOSS WILD-TYPE 67  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     35    1
  13Q LOSS WILD-TYPE   67    2
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               35                 67
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED   43  2 11
  13Q LOSS WILD-TYPE 77  1 26
D65V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               43                 77
  M1                2                  1
  MX               11                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   21 35
  13Q LOSS WILD-TYPE 39 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     21   35
  13Q LOSS WILD-TYPE   39   65
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               21                 39
  MALE                 35                 65
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  13Q LOSS MUTATED                         1                       53
  13Q LOSS WILD-TYPE                       1                      103
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  13Q LOSS MUTATED                                  2
  13Q LOSS WILD-TYPE                                0
D65V8, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       53                103
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED   42  5  0  7
  13Q LOSS WILD-TYPE 89  6  1  5
D65V9, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               42                 89
  R1                5                  6
  R2                0                  1
  RX                7                  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
  13Q LOSS MUTATED                                  0    18
  13Q LOSS WILD-TYPE                                1    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           2    36
  13Q LOSS WILD-TYPE                         6    73
D65V10, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          18                 18
  BLACK OR AFRICAN AMERICAN                       2                  6
  WHITE                                          36                 73
[1] 4 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    1 51
  13Q LOSS WILD-TYPE  2 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   51
  13Q LOSS WILD-TYPE    2   92
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               51                 92
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   26 21
  14Q LOSS WILD-TYPE 65 45
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                47                110 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                21                 45 
$`14Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       37.32        10.13        27.52         5.03        13.84         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3MA 
       22.36         0.07         2.86         0.39         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A 
        0.10         0.13        79.73        83.57       113.00         2.60 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       21.76        90.71        45.11        29.16        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NH 
        5.62         7.66        13.78        30.61        32.52        14.24 
TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ 
       18.44        73.81        12.26        13.41         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X 
        0.20        10.98        11.93        60.36         1.22        58.49 
TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-NI-A8LF 
       25.64         4.37         1.84        13.38        16.37 

$`14Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        27.91        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A5W4 TCGA-BC-A69H 
       23.34         1.12        69.57        44.42         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A116 
       12.72         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        14.07 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR 
       15.06        39.78        56.25        29.56        93.67         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
        1.45        27.72       100.96        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
       13.35         0.23         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        11.74         0.62         9.96        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        14.86        21.53        22.13         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 
       19.23        14.70        11.97         7.99         7.76         5.98 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG 
        1.02         2.66         4.01         2.14        11.84         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57         5.10        14.24        12.85         8.71         1.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            113.00             107.11 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             13.41              14.50 
[1] "0.1 - 113.0 (13.4)" "0.0 - 107.1 (14.5)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED        13       15         0         11          3
  14Q LOSS WILD-TYPE      52       22         2         20          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q LOSS MUTATED            2        0         0         1
  14Q LOSS WILD-TYPE          3        1         1         1
D66V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  13                 52
  STAGE II                 15                 22
  STAGE III                 0                  2
  STAGE IIIA               11                 20
  STAGE IIIB                3                  2
  STAGE IIIC                2                  3
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED   14 16 16  3
  14Q LOSS WILD-TYPE 54 25 26  5
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               14                 54
  T2               16                 25
  T3               16                 26
  T4                3                  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"
D66V5, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   30  1
  14Q LOSS WILD-TYPE 72  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     30    1
  14Q LOSS WILD-TYPE   72    2
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               30                 72
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  14Q LOSS MUTATED   39  1  9
  14Q LOSS WILD-TYPE 81  2 28
D66V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               39                 81
  M1                1                  2
  MX                9                 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"
D66V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   16 33
  14Q LOSS WILD-TYPE 44 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     16   33
  14Q LOSS WILD-TYPE   44   67
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               16                 44
  MALE                 33                 67
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  14Q LOSS MUTATED                         1                       48
  14Q LOSS WILD-TYPE                       1                      108
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  14Q LOSS MUTATED                                  0
  14Q LOSS WILD-TYPE                                2
D66V8, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       48                108
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS MUTATED   37  4  0  6
  14Q LOSS WILD-TYPE 94  7  1  6
D66V9, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               37                 94
  R1                4                  7
  R2                0                  1
  RX                6                  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
  14Q LOSS MUTATED                                  0    15
  14Q LOSS WILD-TYPE                                1    21
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           2    30
  14Q LOSS WILD-TYPE                         6    79
D66V10, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          15                 21
  BLACK OR AFRICAN AMERICAN                       2                  6
  WHITE                                          30                 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"
D66V11, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  42
  14Q LOSS WILD-TYPE   2 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   42
  14Q LOSS WILD-TYPE    2  101
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               42                101
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   19 12
  15Q LOSS WILD-TYPE 72 54
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                31                126 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                 54 
$`15Q LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-A3MA TCGA-DD-A113 
        5.03         9.50        14.60         0.07         0.07        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EI TCGA-DD-A1EJ 
       37.78        83.57         2.60        90.71         6.02        29.16 
TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A4NA TCGA-DD-A4NQ TCGA-DD-A73B 
       13.64         5.62       102.74        33.14        12.26         9.30 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KB 
       13.41         0.23         0.20         0.20         0.20        10.98 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25Z TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-KR-A7K2 
        0.33        60.36        21.53         4.37         1.84        11.84 
TCGA-KR-A7K7 
       13.38 

$`15Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-CC-5260 
       44.42        13.84         0.26        22.36        12.72         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-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
        0.13        53.33       113.00         7.33         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-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39X 
       12.95        45.11        49.15        18.35        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-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 
       14.07        14.24        18.44        15.06        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        93.67         0.30        80.75        66.35 
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-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP 
       12.69        15.85        13.91        13.35         0.20         0.20 
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-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-A25S 
        8.12         6.38         0.13         0.03         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-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-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
       11.97         7.99         7.76         5.98         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        4.01         2.14         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         8.71         1.71        58.88        16.37         4.44 

  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 
             10.98              14.78 
[1] "0.1 - 102.7 (11.0)" "0.0 - 113.0 (14.8)"
[1] "hr=" "1"  
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  15Q LOSS MUTATED        10       11         1          7          1
  15Q LOSS WILD-TYPE      55       26         1         24          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q LOSS MUTATED            2        0         0         0
  15Q LOSS WILD-TYPE          3        1         1         2
D67V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  10                 55
  STAGE II                 11                 26
  STAGE III                 1                  1
  STAGE IIIA                7                 24
  STAGE IIIB                1                  4
  STAGE IIIC                2                  3
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED   11 12 10  0
  15Q LOSS WILD-TYPE 57 29 32  8
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               11                 57
  T2               12                 29
  T3               10                 32
  T4                0                  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"
D67V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   18  2
  15Q LOSS WILD-TYPE 84  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     18    2
  15Q LOSS WILD-TYPE   84    1
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               18                 84
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED   29  0  4
  15Q LOSS WILD-TYPE 91  3 33
D67V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               29                 91
  M1                0                  3
  MX                4                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   11 22
  15Q LOSS WILD-TYPE 49 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     11   22
  15Q LOSS WILD-TYPE   49   78
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               11                 49
  MALE                 22                 78
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  15Q LOSS MUTATED                         0                       32
  15Q LOSS WILD-TYPE                       2                      124
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  15Q LOSS MUTATED                                  1
  15Q LOSS WILD-TYPE                                1
D67V8, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       32                124
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    28   2   0   3
  15Q LOSS WILD-TYPE 103   9   1   9
D67V9, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               28                103
  R1                2                  9
  R2                0                  1
  RX                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0    11
  15Q LOSS WILD-TYPE                                1    25
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           3    19
  15Q LOSS WILD-TYPE                         5    90
D67V10, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          11                 25
  BLACK OR AFRICAN AMERICAN                       3                  5
  WHITE                                          19                 90
[1] 4 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     2  28
  15Q LOSS WILD-TYPE   1 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   28
  15Q LOSS WILD-TYPE    1  115
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               28                115
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED   23 20
  16P LOSS WILD-TYPE 68 46
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                43                114 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                20                 46 
$`16P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.84         9.50        14.60         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A11B 
        3.39         0.10         0.10         0.13        37.78         0.46 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z 
       12.95        49.15         6.02        29.16         5.62        19.76 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NN 
        0.36        30.61        73.38        14.24        18.44        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       73.81        12.26         9.30        15.85        13.35         0.23 
TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 
        0.20         0.20        10.98        22.85        32.45        27.88 
TCGA-FV-A3R2 TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-MI-A75G 
        6.38        58.49        14.86         1.84        13.38        14.24 
TCGA-MI-A75I 
        8.71 

$`16P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-CC-5263 
        5.03        44.42         0.26        22.36        12.72         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        14.07        15.06        39.78        56.25        93.67 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        66.35        10.98         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 
        1.45        27.72       100.96        13.41        12.69        13.91 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       11.74         0.62         9.96        11.93        14.40        19.10 
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-A25Z 
        1.22        51.06        53.79        28.27        30.74        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 
       11.97         7.99         4.37         7.76         5.98         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75C 
        2.66         4.01         2.14        11.84         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        5.10        12.85         1.71        58.88        16.37         4.44 

  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 
             12.95              14.88 
[1] "0.1 - 73.8 (12.9)"  "0.0 - 113.0 (14.9)"
[1] "hr=" "1.8"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P LOSS MUTATED        13       16         1          8          2
  16P LOSS WILD-TYPE      52       21         1         23          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P LOSS MUTATED            3        0         1         1
  16P LOSS WILD-TYPE          2        1         0         1
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  13                 52
  STAGE II                 16                 21
  STAGE III                 1                  1
  STAGE IIIA                8                 23
  STAGE IIIB                2                  3
  STAGE IIIC                3                  2
  STAGE IV                  0                  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                 T1 T2 T3 T4
  16P LOSS MUTATED   15 17 11  3
  16P LOSS WILD-TYPE 53 24 31  5
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               15                 53
  T2               17                 24
  T3               11                 31
  T4                3                  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"
D68V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   29  2
  16P LOSS WILD-TYPE 73  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     29    2
  16P LOSS WILD-TYPE   73    1
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               29                 73
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16P LOSS MUTATED   38  1  7
  16P LOSS WILD-TYPE 82  2 30
D68V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               38                 82
  M1                1                  2
  MX                7                 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"
D68V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   19 27
  16P LOSS WILD-TYPE 41 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     19   27
  16P LOSS WILD-TYPE   41   73
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               19                 41
  MALE                 27                 73
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16P LOSS MUTATED                         0                       45
  16P LOSS WILD-TYPE                       2                      111
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16P LOSS MUTATED                                  1
  16P LOSS WILD-TYPE                                1
D68V8, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       45                111
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  16P LOSS MUTATED   38  1  0  6
  16P LOSS WILD-TYPE 93 10  1  6
D68V9, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               38                 93
  R1                1                 10
  R2                0                  1
  RX                6                  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
  16P LOSS MUTATED                                  0    17
  16P LOSS WILD-TYPE                                1    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           2    26
  16P LOSS WILD-TYPE                         6    83
D68V10, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          17                 19
  BLACK OR AFRICAN AMERICAN                       2                  6
  WHITE                                          26                 83
[1] 4 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     2  41
  16P LOSS WILD-TYPE   1 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2   41
  16P LOSS WILD-TYPE    1  102
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  1
  NOT HISPANIC OR LATINO               41                102
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   30 24
  16Q LOSS WILD-TYPE 61 42
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                54                103 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                24                 42 
$`16Q LOSS MUTATED`
TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
       46.78         2.99        44.42        13.84        22.36        14.60 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC 
        0.07         2.86         0.39         4.24         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF 
       79.73        37.78        53.33         2.60         0.46        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A8 
       49.15         6.02        29.16         5.62        19.76         0.36 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NN TCGA-DD-A4NO 
       30.61        73.38        14.24        18.44        29.56        73.81 
TCGA-DD-A4NQ TCGA-DD-A73B TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       12.26         9.30        13.41        15.85        13.35         0.23 
TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 
        0.20         0.20        10.98        22.85        32.45        27.88 
TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
        6.38         1.22        53.79        58.49        14.86        25.64 
TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-O8-A75V 
       14.70         1.84        13.38        14.24         8.71         4.44 

$`16Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF 
       25.32        23.34         1.12        69.57         5.03         0.26 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        9.50        12.72         3.39         3.32         0.10         0.07 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       83.57       113.00         7.33        21.76        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-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        13.64        21.14        55.69        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        32.52        14.07        15.06        39.78        56.25 
TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       93.67         0.30        80.75        66.35        10.98         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A627 
       10.98         1.45        27.72       100.96        12.69        13.91 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       11.74         0.62         9.96        11.93        14.40        19.10 
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-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       51.06        28.27        30.74        21.53        22.13         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.53        19.23        11.97         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        5.98         1.02         2.66         4.01         2.14        11.84 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
        0.49         9.57         5.10        12.85         1.71        58.88 
TCGA-NI-A8LF 
       16.37 

  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 
            13.625             14.070 
[1] "0.1 - 79.7 (13.6)"  "0.0 - 113.0 (14.1)"
[1] "hr=" "1.4"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED        17       20         1         10          2
  16Q LOSS WILD-TYPE      48       17         1         21          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q LOSS MUTATED            2        0         1         1
  16Q LOSS WILD-TYPE          3        1         0         1
D69V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  17                 48
  STAGE II                 20                 17
  STAGE III                 1                  1
  STAGE IIIA               10                 21
  STAGE IIIB                2                  3
  STAGE IIIC                2                  3
  STAGE IV                  0                  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                 T1 T2 T3 T4
  16Q LOSS MUTATED   19 21 14  3
  16Q LOSS WILD-TYPE 49 20 28  5
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               19                 49
  T2               21                 20
  T3               14                 28
  T4                3                  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"
D69V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   37  2
  16Q LOSS WILD-TYPE 65  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     37    2
  16Q LOSS WILD-TYPE   65    1
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               37                 65
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16Q LOSS MUTATED   46  1 10
  16Q LOSS WILD-TYPE 74  2 27
D69V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               46                 74
  M1                1                  2
  MX               10                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   23 34
  16Q LOSS WILD-TYPE 37 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     23   34
  16Q LOSS WILD-TYPE   37   66
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               23                 37
  MALE                 34                 66
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16Q LOSS MUTATED                         0                       56
  16Q LOSS WILD-TYPE                       2                      100
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16Q LOSS MUTATED                                  1
  16Q LOSS WILD-TYPE                                1
D69V8, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       56                100
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  16Q LOSS MUTATED   47  3  0  7
  16Q LOSS WILD-TYPE 84  8  1  5
D69V9, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               47                 84
  R1                3                  8
  R2                0                  1
  RX                7                  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
  16Q LOSS MUTATED                                  0    22
  16Q LOSS WILD-TYPE                                1    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           3    30
  16Q LOSS WILD-TYPE                         5    79
D69V10, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          22                 14
  BLACK OR AFRICAN AMERICAN                       3                  5
  WHITE                                          30                 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"
D69V11, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3 50
  16Q LOSS WILD-TYPE  0 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   50
  16Q LOSS WILD-TYPE    0   93
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  0
  NOT HISPANIC OR LATINO               50                 93
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   40 36
  17P LOSS WILD-TYPE 51 30
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                76                 81 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                36                 30 
$`17P LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z 
       48.99        27.91        10.13        27.52        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
       69.57         5.03        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       14.60         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        3.32         0.10         0.13        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         2.60        21.76        51.29        79.40        66.31 
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-A39Y TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A4NA 
        5.62        25.81        17.59        20.12       102.74        33.14 
TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NQ TCGA-DD-A73B 
       32.52        14.24        18.44        15.06        12.26         9.30 
TCGA-DD-A73E TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KC 
        1.45        13.41         0.20         0.20         0.20         0.62 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25U 
       32.45        19.10        27.88         0.03         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SL TCGA-G3-A5SM 
       28.27        14.86        21.53        25.64         7.99         4.37 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75E 
        1.84         1.02         2.14        11.84         0.49         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24         8.71        58.88         4.44 

$`17P LOSS WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A216 
       37.32        46.78        27.52         2.99        25.32        44.42 
TCGA-BC-A69I TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11B 
       12.72         0.10         0.07        79.73        37.78         0.46 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V 
       90.71        19.79        75.65         6.71        12.95        21.14 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A7 
       55.69        19.76         7.66        70.06       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL 
        0.36        30.61        73.38        14.07        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        93.67         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI 
       10.98         7.56        10.98        27.72       100.96        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP 
       15.85        13.91        13.35         0.23         0.20         0.20 
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-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K7 TCGA-MI-A75C 
        7.76         5.98         2.66         4.01        13.38         9.57 
TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A8LF 
       12.85         1.71        16.37 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            113.00             107.11 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             13.74              14.07 
[1] "0.0 - 113.0 (13.7)" "0.1 - 107.1 (14.1)"
[1] "hr=" "1.5"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED        25       21         2         15          2
  17P LOSS WILD-TYPE      40       16         0         16          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P LOSS MUTATED            5        1         1         1
  17P LOSS WILD-TYPE          0        0         0         1
D70V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  25                 40
  STAGE II                 21                 16
  STAGE III                 2                  0
  STAGE IIIA               15                 16
  STAGE IIIB                2                  3
  STAGE IIIC                5                  0
  STAGE IV                  1                  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                 T1 T2 T3 T4
  17P LOSS MUTATED   28 24 22  5
  17P LOSS WILD-TYPE 40 17 20  3
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               28                 40
  T2               24                 17
  T3               22                 20
  T4                5                  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"
D70V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   50  3
  17P LOSS WILD-TYPE 52  0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     50    3
  17P LOSS WILD-TYPE   52    0
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               50                 52
  1                3                  0
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED   62  2 15
  17P LOSS WILD-TYPE 58  1 22
D70V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               62                 58
  M1                2                  1
  MX               15                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   27 52
  17P LOSS WILD-TYPE 33 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     27   52
  17P LOSS WILD-TYPE   33   48
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               27                 33
  MALE                 52                 48
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17P LOSS MUTATED                         1                       76
  17P LOSS WILD-TYPE                       1                       80
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17P LOSS MUTATED                                  2
  17P LOSS WILD-TYPE                                0
D70V8, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       76                 80
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   61  6  1  9
  17P LOSS WILD-TYPE 70  5  0  3
D70V9, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               61                 70
  R1                6                  5
  R2                1                  0
  RX                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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0    23
  17P LOSS WILD-TYPE                                1    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           5    49
  17P LOSS WILD-TYPE                         3    60
D70V10, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          23                 13
  BLACK OR AFRICAN AMERICAN                       5                  3
  WHITE                                          49                 60
[1] 4 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    3 70
  17P LOSS WILD-TYPE  0 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3   70
  17P LOSS WILD-TYPE    0   73
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  0
  NOT HISPANIC OR LATINO               70                 73
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   13  7
  17Q LOSS WILD-TYPE 78 59
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                20                137 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                 59 
$`17Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A5W4 TCGA-DD-A116 TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EJ 
       10.13         9.50        53.33        66.31        45.11        29.16 
TCGA-DD-A3A0 TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-ED-A7PZ 
       25.81        32.52        14.24        18.44        15.06         0.20 
TCGA-ED-A82E TCGA-FV-A3I0 TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-KR-A7K0 
        0.20        27.88         7.99         4.37         1.84         2.14 
TCGA-KR-A7K2 TCGA-MI-A75G 
       11.84        14.24 

$`17Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84         0.26        22.36        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        90.71        79.40        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        49.15         6.02        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       33.14        73.38        14.07        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
        0.23         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-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-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
       14.70        11.97         7.76         5.98         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
        4.01        13.38         0.49         9.57         5.10        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71         1.71        58.88        16.37         4.44 

  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 
             14.24              13.84 
[1] "0.2 - 66.3 (14.2)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1"  
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q LOSS MUTATED         6        6         0          4          2
  17Q LOSS WILD-TYPE      59       31         2         27          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q LOSS MUTATED            1        0         1         0
  17Q LOSS WILD-TYPE          4        1         0         2
D71V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   6                 59
  STAGE II                  6                 31
  STAGE III                 0                  2
  STAGE IIIA                4                 27
  STAGE IIIB                2                  3
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    8  6  7  0
  17Q LOSS WILD-TYPE 60 35 35  8
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                8                 60
  T2                6                 35
  T3                7                 35
  T4                0                  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"
D71V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   10  2
  17Q LOSS WILD-TYPE 92  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10    2
  17Q LOSS WILD-TYPE   92    1
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               10                 92
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17Q LOSS MUTATED    18   0   3
  17Q LOSS WILD-TYPE 102   3  34
D71V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0               18                102
  M1                0                  3
  MX                3                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    7 14
  17Q LOSS WILD-TYPE 53 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7   14
  17Q LOSS WILD-TYPE   53   86
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                7                 53
  MALE                 14                 86
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17Q LOSS MUTATED                         1                       18
  17Q LOSS WILD-TYPE                       1                      138
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17Q LOSS MUTATED                                  2
  17Q LOSS WILD-TYPE                                0
D71V8, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       18                138
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    20   1   0   0
  17Q LOSS WILD-TYPE 111  10   1  12
D71V9, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               20                111
  R1                1                 10
  R2                0                  1
  RX                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     3
  17Q LOSS WILD-TYPE                                1    33
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           0    17
  17Q LOSS WILD-TYPE                         8    92
D71V10, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                 33
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                          17                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  18
  17Q LOSS WILD-TYPE   3 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   18
  17Q LOSS WILD-TYPE    3  125
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               18                125
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   19 11
  18P LOSS WILD-TYPE 72 55
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                30                127 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                11                 55 
$`18P LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A 
       10.13         5.03        13.84         0.10       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
        0.46        12.95        29.16        13.64        55.69         5.62 
TCGA-DD-A3A4 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73E TCGA-DD-A73G 
       20.12        32.52        18.44        73.81         1.45       100.96 
TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ES-A2HS TCGA-FV-A3I0 
       13.41         0.20         0.20         0.20        22.85        27.88 
TCGA-FV-A496 TCGA-G3-A25S TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MR-A8JO TCGA-NI-A8LF 
        0.33         1.22        13.38        14.24         1.71        16.37 

$`18P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-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-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-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-A1EH TCGA-DD-A1EI 
       19.79        75.65         6.71        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       18.35        21.14        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       17.59       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        73.38        14.07        14.24        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       66.35        10.98         9.30         7.56        10.98        27.72 
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-A7PZ TCGA-ED-A8O5 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-A2QR 
        0.62         9.96        11.93        14.40        32.45        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        8.12         6.38         0.13         0.03        60.36         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-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-A7M7 
       14.70        11.97         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         9.57         5.10        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.10               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            113.00             107.11 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            13.395             14.400 
[1] "0.1 - 113.0 (13.4)" "0.0 - 107.1 (14.4)"
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED        15       10         0          3          0
  18P LOSS WILD-TYPE      50       27         2         28          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P LOSS MUTATED            1        0         0         0
  18P LOSS WILD-TYPE          4        1         1         2
D72V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  15                 50
  STAGE II                 10                 27
  STAGE III                 0                  2
  STAGE IIIA                3                 28
  STAGE IIIB                0                  5
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED   16 10  5  0
  18P LOSS WILD-TYPE 52 31 37  8
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               16                 52
  T2               10                 31
  T3                5                 37
  T4                0                  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"
D72V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   18  1
  18P LOSS WILD-TYPE 84  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     18    1
  18P LOSS WILD-TYPE   84    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               18                 84
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED   25  0  6
  18P LOSS WILD-TYPE 95  3 31
D72V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               25                 95
  M1                0                  3
  MX                6                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   13 18
  18P LOSS WILD-TYPE 47 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     13   18
  18P LOSS WILD-TYPE   47   82
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               13                 47
  MALE                 18                 82
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18P LOSS MUTATED                         2                       28
  18P LOSS WILD-TYPE                       0                      128
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18P LOSS MUTATED                                  1
  18P LOSS WILD-TYPE                                1
D72V8, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       28                128
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    27   1   0   3
  18P LOSS WILD-TYPE 104  10   1   9
D72V9, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               27                104
  R1                1                 10
  R2                0                  1
  RX                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     6
  18P LOSS WILD-TYPE                                1    30
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           2    23
  18P LOSS WILD-TYPE                         6    86
D72V10, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 30
  BLACK OR AFRICAN AMERICAN                       2                  6
  WHITE                                          23                 86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     0  28
  18P LOSS WILD-TYPE   3 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0   28
  18P LOSS WILD-TYPE    3  115
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               28                115
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   20 12
  18Q LOSS WILD-TYPE 71 54
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                32                125 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                12                 54 
$`18Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-CC-A3MB TCGA-DD-A118 
       10.13         5.03        44.42        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-A3A9 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73B 
        5.62        30.61        32.52        18.44        73.81         9.30 
TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7XP TCGA-ED-A82E 
        1.45       100.96        13.41        13.35         0.20         0.20 
TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S TCGA-KR-A7K7 TCGA-MI-A75G 
       22.85        27.88         0.33         1.22        13.38        14.24 
TCGA-MR-A8JO TCGA-NI-A8LF 
        1.71        16.37 

$`18Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KF 
        2.99        25.32        23.34         1.12        69.57         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       22.36         9.50        14.60        12.72         0.07         2.86 
TCGA-CC-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        14.07        14.24        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         7.56        10.98        27.72        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A8O5 
       13.91         0.23         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-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.93        14.40        32.45        19.10         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        0.13         0.03        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-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75C 
        2.66         4.01         2.14        11.84         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        12.85         8.71        58.88         4.44 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.10               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            113.00             107.11 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            13.395             14.400 
[1] "0.1 - 113.0 (13.4)" "0.0 - 107.1 (14.4)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED        16        9         0          4          0
  18Q LOSS WILD-TYPE      49       28         2         27          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q LOSS MUTATED            1        0         0         1
  18Q LOSS WILD-TYPE          4        1         1         1
D73V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  16                 49
  STAGE II                  9                 28
  STAGE III                 0                  2
  STAGE IIIA                4                 27
  STAGE IIIB                0                  5
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED   17  9  6  1
  18Q LOSS WILD-TYPE 51 32 36  7
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               17                 51
  T2                9                 32
  T3                6                 36
  T4                1                  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"
D73V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   20  1
  18Q LOSS WILD-TYPE 82  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     20    1
  18Q LOSS WILD-TYPE   82    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               20                 82
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED   26  1  6
  18Q LOSS WILD-TYPE 94  2 31
D73V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               26                 94
  M1                1                  2
  MX                6                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   15 18
  18Q LOSS WILD-TYPE 45 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     15   18
  18Q LOSS WILD-TYPE   45   82
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               15                 45
  MALE                 18                 82
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18Q LOSS MUTATED                         2                       30
  18Q LOSS WILD-TYPE                       0                      126
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18Q LOSS MUTATED                                  1
  18Q LOSS WILD-TYPE                                1
D73V8, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       30                126
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED    29   1   0   3
  18Q LOSS WILD-TYPE 102  10   1   9
D73V9, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               29                102
  R1                1                 10
  R2                0                  1
  RX                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     6
  18Q LOSS WILD-TYPE                                1    30
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           2    25
  18Q LOSS WILD-TYPE                         6    84
D73V10, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 30
  BLACK OR AFRICAN AMERICAN                       2                  6
  WHITE                                          25                 84
[1] 4 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     1  28
  18Q LOSS WILD-TYPE   2 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1   28
  18Q LOSS WILD-TYPE    2  115
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               28                115
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    8  8
  19P LOSS WILD-TYPE 83 58
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                141 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 8                 58 
$`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        15.06 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A3CH 
        0.33        60.36         1.22        25.64 

$`19P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
       27.52        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5260 
       13.84        22.36         9.50        14.60        12.72         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        0.39         3.39         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-A1EF TCGA-DD-A1EH TCGA-DD-A1EK 
       19.79        75.65         6.71        12.95        49.15        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        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       14.24        18.44        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
        8.12         6.38         0.13         0.03         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-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-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57         5.10        14.24        12.85         8.71         1.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.07               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             60.36             113.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             4.635             14.240 
[1] "0.1 - 60.4 (4.6)"   "0.0 - 113.0 (14.2)"
[1] "hr=" "2.2"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED         8        2         0          4          0
  19P LOSS WILD-TYPE      57       35         2         27          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P LOSS MUTATED            1        0         0         0
  19P LOSS WILD-TYPE          4        1         1         2
D74V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   8                 57
  STAGE II                  2                 35
  STAGE III                 0                  2
  STAGE IIIA                4                 27
  STAGE IIIB                0                  5
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    9  2  5  1
  19P LOSS WILD-TYPE 59 39 37  7
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                9                 59
  T2                2                 39
  T3                5                 37
  T4                1                  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"
D74V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    9  1
  19P LOSS WILD-TYPE 93  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9    1
  19P LOSS WILD-TYPE   93    2
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                9                 93
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19P LOSS MUTATED    14   0   3
  19P LOSS WILD-TYPE 106   3  34
D74V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               14                106
  M1                0                  3
  MX                3                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    4 13
  19P LOSS WILD-TYPE 56 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4   13
  19P LOSS WILD-TYPE   56   87
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                4                 56
  MALE                 13                 87
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19P LOSS MUTATED                         0                       17
  19P LOSS WILD-TYPE                       2                      139
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19P LOSS MUTATED                                  0
  19P LOSS WILD-TYPE                                2
D74V8, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       17                139
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    10   3   0   3
  19P LOSS WILD-TYPE 121   8   1   9
D74V9, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               10                121
  R1                3                  8
  R2                0                  1
  RX                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     7
  19P LOSS WILD-TYPE                                1    29
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           1     9
  19P LOSS WILD-TYPE                         7   100
D74V10, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 29
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                           9                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0  16
  19P LOSS WILD-TYPE   3 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   16
  19P LOSS WILD-TYPE    3  127
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               16                127
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    6  5
  19Q LOSS WILD-TYPE 85 61
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                11                146 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                 61 
$`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-FV-A4ZP 
        6.02        29.16         5.62        15.06        60.36 

$`19Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36         9.50        14.60        12.72 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        2.86         0.39         3.39         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-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-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-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        14.07        14.24        18.44        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         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         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        5.10        14.24        12.85         8.71         1.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             60.36             113.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              5.03              14.24 
[1] "0.1 - 60.4 (5.0)"   "0.0 - 113.0 (14.2)"
[1] "hr=" "2.1"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED         5        2         0          3          0
  19Q LOSS WILD-TYPE      60       35         2         28          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q LOSS MUTATED            1        0         0         0
  19Q LOSS WILD-TYPE          4        1         1         2
D75V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   5                 60
  STAGE II                  2                 35
  STAGE III                 0                  2
  STAGE IIIA                3                 28
  STAGE IIIB                0                  5
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS MUTATED    6  2  4  0
  19Q LOSS WILD-TYPE 62 39 38  8
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                6                 62
  T2                2                 39
  T3                4                 38
  T4                0                  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"
D75V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    6  1
  19Q LOSS WILD-TYPE 96  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    1
  19Q LOSS WILD-TYPE   96    2
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                6                 96
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19Q LOSS MUTATED    10   0   2
  19Q LOSS WILD-TYPE 110   3  35
D75V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               10                110
  M1                0                  3
  MX                2                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  9
  19Q LOSS WILD-TYPE 57 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    9
  19Q LOSS WILD-TYPE   57   91
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 57
  MALE                  9                 91
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19Q LOSS MUTATED                         0                       12
  19Q LOSS WILD-TYPE                       2                      144
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19Q LOSS MUTATED                                  0
  19Q LOSS WILD-TYPE                                2
D75V8, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       12                144
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED     7   1   0   3
  19Q LOSS WILD-TYPE 124  10   1   9
D75V9, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                7                124
  R1                1                 10
  R2                0                  1
  RX                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     5
  19Q LOSS WILD-TYPE                                1    31
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           1     6
  19Q LOSS WILD-TYPE                         7   103
D75V10, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 31
  BLACK OR AFRICAN AMERICAN                       1                  7
  WHITE                                           6                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0  11
  19Q LOSS WILD-TYPE   3 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   11
  19Q LOSS WILD-TYPE    3  132
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               11                132
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    5  5
  20P LOSS WILD-TYPE 86 61
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                10                147 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                 61 
$`20P LOSS MUTATED`
TCGA-BC-A10Z TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A1EK TCGA-DD-A39Y TCGA-DD-A3A3 
        1.12         0.13        79.73        18.35         5.62        17.59 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-ED-A8O5 TCGA-MR-A8JO 
       73.81        12.26         0.20         1.71 

$`20P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 
       27.52         2.99        25.32        23.34        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       12.72         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.10         0.07         0.10        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-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-A3A7 TCGA-DD-A3A8 
       70.06        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        73.38        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       18.44        15.06        39.78        56.25        29.56        93.67 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-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-A7M7 TCGA-G3-A7M9 
       11.97         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.13               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             79.73             113.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              8.94              14.07 
[1] "0.1 - 79.7 (8.9)"   "0.0 - 113.0 (14.1)"
[1] "hr=" "1.5"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P LOSS MUTATED         5        2         0          2          0
  20P LOSS WILD-TYPE      60       35         2         29          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P LOSS MUTATED            0        0         0         1
  20P LOSS WILD-TYPE          5        1         1         1
D76V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   5                 60
  STAGE II                  2                 35
  STAGE III                 0                  2
  STAGE IIIA                2                 29
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    5  2  2  1
  20P LOSS WILD-TYPE 63 39 40  7
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                5                 63
  T2                2                 39
  T3                2                 40
  T4                1                  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"
D76V5, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    9  0
  20P LOSS WILD-TYPE 93  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      9    0
  20P LOSS WILD-TYPE   93    3
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                9                 93
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  20P LOSS MUTATED     7   1   2
  20P LOSS WILD-TYPE 113   2  35
D76V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                7                113
  M1                1                  2
  MX                2                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    4  6
  20P LOSS WILD-TYPE 56 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4    6
  20P LOSS WILD-TYPE   56   94
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                4                 56
  MALE                  6                 94
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20P LOSS MUTATED                         1                        9
  20P LOSS WILD-TYPE                       1                      147
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20P LOSS MUTATED                                  0
  20P LOSS WILD-TYPE                                2
D76V8, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                        9                147
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED     9   0   0   1
  20P LOSS WILD-TYPE 122  11   1  11
D76V9, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                9                122
  R1                0                 11
  R2                0                  1
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     4
  20P LOSS WILD-TYPE                                1    32
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           0     6
  20P LOSS WILD-TYPE                         8   103
D76V10, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                 32
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                           6                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1   8
  20P LOSS WILD-TYPE   2 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    8
  20P LOSS WILD-TYPE    2  135
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO                8                135
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    4  2
  20Q LOSS WILD-TYPE 87 64
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                151 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 64 
$`20Q LOSS MUTATED`
TCGA-DD-A113 TCGA-DD-A39Y TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-ED-A8O5 TCGA-MR-A8JO 
       79.73         5.62        73.81        12.26         0.20         1.71 

$`20Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        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-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-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         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-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-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        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56        93.67         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-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         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF 
        5.10        14.24        12.85         8.71        58.88        16.37 
TCGA-O8-A75V 
        4.44 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.20               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             79.73             113.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              8.94              14.07 
[1] "0.2 - 79.7 (8.9)"   "0.0 - 113.0 (14.1)"
[1] "hr=" "1.4"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q LOSS MUTATED         3        2         0          1          0
  20Q LOSS WILD-TYPE      62       35         2         30          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q LOSS MUTATED            0        0         0         0
  20Q LOSS WILD-TYPE          5        1         1         2
D77V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   3                 62
  STAGE II                  2                 35
  STAGE III                 0                  2
  STAGE IIIA                1                 30
  STAGE IIIB                0                  5
  STAGE IIIC                0                  5
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20Q LOSS MUTATED    3  2  1  0
  20Q LOSS WILD-TYPE 65 39 41  8
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                3                 65
  T2                2                 39
  T3                1                 41
  T4                0                  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"
D77V5, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    5  0
  20Q LOSS WILD-TYPE 97  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    0
  20Q LOSS WILD-TYPE   97    3
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                5                 97
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  20Q LOSS MUTATED     5   0   1
  20Q LOSS WILD-TYPE 115   3  36
D77V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                5                115
  M1                0                  3
  MX                1                 36
[1] 3 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    2  4
  20Q LOSS WILD-TYPE 58 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    4
  20Q LOSS WILD-TYPE   58   96
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                 58
  MALE                  4                 96
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20Q LOSS MUTATED                         1                        5
  20Q LOSS WILD-TYPE                       1                      151
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20Q LOSS MUTATED                                  0
  20Q LOSS WILD-TYPE                                2
D77V8, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                        5                151
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     5   0   0   1
  20Q LOSS WILD-TYPE 126  11   1  11
D77V9, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                5                126
  R1                0                 11
  R2                0                  1
  RX                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     2
  20Q LOSS WILD-TYPE                                1    34
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           0     4
  20Q LOSS WILD-TYPE                         8   105
D77V10, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                 34
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                           4                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   4
  20Q LOSS WILD-TYPE   2 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    4
  20Q LOSS WILD-TYPE    2  139
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO                4                139
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   21 21
  21Q LOSS WILD-TYPE 70 45
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                42                115 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                21                 45 
$`21Q LOSS MUTATED`
TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A69H TCGA-CC-5262 TCGA-CC-A1HT 
       27.52         5.03        44.42        14.60         3.39         3.32 
TCGA-CC-A3MB TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EG 
        0.10         7.33         2.60        90.71        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A0 
       49.15        29.16        13.64        21.14         5.62        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A73G 
        7.66        13.78        30.61        32.52        18.44       100.96 
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-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25Z 
       11.93        32.45         0.33        60.36         1.22        21.53 
TCGA-G3-A7M9 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MR-A8JO 
        1.84         2.14        13.38         0.49         5.10         1.71 

$`21Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A217 
        2.99        25.32        23.34         1.12        69.57        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
        0.26        22.36         9.50        12.72         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 
       14.07        14.24        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 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-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       22.85        14.40        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-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         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K2 
        7.76         5.98         1.02         2.66         4.01        11.84 
TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF 
        9.57        14.24        12.85         8.71        58.88        16.37 
TCGA-O8-A75V 
        4.44 

  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 
             12.44              14.70 
[1] "0.1 - 101.0 (12.4)" "0.0 - 113.0 (14.7)"
[1] "hr=" "1.7"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED        15       10         1          8          2
  21Q LOSS WILD-TYPE      50       27         1         23          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q LOSS MUTATED            3        1         1         1
  21Q LOSS WILD-TYPE          2        0         0         1
D78V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  15                 50
  STAGE II                 10                 27
  STAGE III                 1                  1
  STAGE IIIA                8                 23
  STAGE IIIB                2                  3
  STAGE IIIC                3                  2
  STAGE IV                  1                  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                 T1 T2 T3 T4
  21Q LOSS MUTATED   17 11 13  3
  21Q LOSS WILD-TYPE 51 30 29  5
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               17                 51
  T2               11                 30
  T3               13                 29
  T4                3                  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"
D78V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   25  2
  21Q LOSS WILD-TYPE 77  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     25    2
  21Q LOSS WILD-TYPE   77    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               25                 77
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED   34  2  8
  21Q LOSS WILD-TYPE 86  1 29
D78V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               34                 86
  M1                2                  1
  MX                8                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   11 33
  21Q LOSS WILD-TYPE 49 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     11   33
  21Q LOSS WILD-TYPE   49   67
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               11                 49
  MALE                 33                 67
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  21Q LOSS MUTATED                         2                       42
  21Q LOSS WILD-TYPE                       0                      114
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  21Q LOSS MUTATED                                  0
  21Q LOSS WILD-TYPE                                2
D78V8, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       42                114
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   34  3  1  2
  21Q LOSS WILD-TYPE 97  8  0 10
D78V9, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               34                 97
  R1                3                  8
  R2                1                  0
  RX                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0    11
  21Q LOSS WILD-TYPE                                1    25
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           3    28
  21Q LOSS WILD-TYPE                         5    81
D78V10, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          11                 25
  BLACK OR AFRICAN AMERICAN                       3                  5
  WHITE                                          28                 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"
D78V11, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     0  38
  21Q LOSS WILD-TYPE   3 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0   38
  21Q LOSS WILD-TYPE    3  105
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               38                105
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   22 12
  22Q LOSS WILD-TYPE 69 54
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                34                123 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                12                 54 
$`22Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-5260 
       37.32        27.52        13.84         0.26         9.50         2.86 
TCGA-CC-A1HT TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A39X TCGA-DD-A39Y 
        3.32        79.73        37.78         2.60        55.69         5.62 
TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP 
      107.11        32.52        18.44        15.06        73.81        93.67 
TCGA-DD-A73B TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-EP-A2KB 
        9.30        13.41         0.23         0.20         0.20        10.98 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-KR-A7K2 
       60.36         1.22        51.06        14.70         1.84        11.84 
TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO 
       13.38        14.24         8.71         1.71 

$`22Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       22.36        14.60        12.72         0.07         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 
        4.24         0.10         0.07         0.10         0.13        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-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       17.59        20.12       102.74        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        73.38        14.07        14.24        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       29.56        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72       100.96        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E 
       15.85        13.91        13.35         0.20         0.20         0.20 
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-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-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-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.99         4.37         7.76         5.98         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
        4.01         2.14         0.49         9.57         5.10        12.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.20               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            107.11             113.00 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            13.395             14.240 
[1] "0.2 - 107.1 (13.4)" "0.0 - 113.0 (14.2)"
[1] "hr=" "1.3"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED        13       12         0          6          1
  22Q LOSS WILD-TYPE      52       25         2         25          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q LOSS MUTATED            1        0         0         0
  22Q LOSS WILD-TYPE          4        1         1         2
D79V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  13                 52
  STAGE II                 12                 25
  STAGE III                 0                  2
  STAGE IIIA                6                 25
  STAGE IIIB                1                  4
  STAGE IIIC                1                  4
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS MUTATED   13 14  7  2
  22Q LOSS WILD-TYPE 55 27 35  6
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               13                 55
  T2               14                 27
  T3                7                 35
  T4                2                  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"
D79V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   21  0
  22Q LOSS WILD-TYPE 81  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     21    0
  22Q LOSS WILD-TYPE   81    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               21                 81
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED   29  0  7
  22Q LOSS WILD-TYPE 91  3 30
D79V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               29                 91
  M1                0                  3
  MX                7                 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"
D79V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   15 21
  22Q LOSS WILD-TYPE 45 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     15   21
  22Q LOSS WILD-TYPE   45   79
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               15                 45
  MALE                 21                 79
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  22Q LOSS MUTATED                         2                       33
  22Q LOSS WILD-TYPE                       0                      123
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  22Q LOSS MUTATED                                  1
  22Q LOSS WILD-TYPE                                1
D79V8, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       33                123
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    26   5   0   4
  22Q LOSS WILD-TYPE 105   6   1   8
D79V9, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               26                105
  R1                5                  6
  R2                0                  1
  RX                4                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0     9
  22Q LOSS WILD-TYPE                                1    27
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           3    24
  22Q LOSS WILD-TYPE                         5    85
D79V10, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                 27
  BLACK OR AFRICAN AMERICAN                       3                  5
  WHITE                                          24                 85
[1] 4 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     1  30
  22Q LOSS WILD-TYPE   2 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   30
  22Q LOSS WILD-TYPE    2  113
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               30                113
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   14  8
  XQ LOSS WILD-TYPE 77 58
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               22               135 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                8                58 
$`XQ LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-A3MA 
       10.13         5.03        13.84         9.50        12.72         0.07 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A4NA TCGA-DD-A4NO 
       37.78        83.57        53.33         0.46        33.14        73.81 
TCGA-DD-A73B TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-FV-A2QR 
        9.30        13.41         0.20         0.20         0.20        19.10 
TCGA-FV-A3I0 TCGA-G3-A6UC TCGA-KR-A7K7 TCGA-MI-A75E 
       27.88         7.76        13.38         5.10 

$`XQ LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        0.26        22.36        14.60         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.10         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D 
       79.73       113.00         7.33         2.60        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-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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        30.61        32.52        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72       100.96        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I1 
        9.96        11.93        22.85        14.40        32.45         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-A7M7 
       19.23        14.70        11.97         7.99         4.37         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        0.49         9.57        14.24        12.85         8.71         1.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  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 
           11.425            14.400 
[1] "0.1 - 83.6 (11.4)"  "0.0 - 113.0 (14.4)"
[1] "hr=" "1"  
D80V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ LOSS MUTATED         5        7         0          5          1          2
  XQ LOSS WILD-TYPE      60       30         2         26          4          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ LOSS MUTATED          0         0         0
  XQ LOSS WILD-TYPE        1         1         2
D80V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  5                60
  STAGE II                 7                30
  STAGE III                0                 2
  STAGE IIIA               5                26
  STAGE IIIB               1                 4
  STAGE IIIC               2                 3
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    5  8  8  1
  XQ LOSS WILD-TYPE 63 33 34  7
D80V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               5                63
  T2               8                33
  T3               8                34
  T4               1                 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"
D80V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   13  1
  XQ LOSS WILD-TYPE 89  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13    1
  XQ LOSS WILD-TYPE   89    2
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              13                89
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  XQ LOSS MUTATED    20   0   2
  XQ LOSS WILD-TYPE 100   3  35
D80V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              20               100
  M1               0                 3
  MX               2                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"
D80V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    8 14
  XQ LOSS WILD-TYPE 52 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8   14
  XQ LOSS WILD-TYPE   52   86
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               8                52
  MALE                14                86
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XQ LOSS MUTATED                         0                       21
  XQ LOSS WILD-TYPE                       2                      135
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XQ LOSS MUTATED                                  1
  XQ LOSS WILD-TYPE                                1
D80V8, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      21               135
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    19   1   0   2
  XQ LOSS WILD-TYPE 112  10   1  10
D80V9, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              19               112
  R1               1                10
  R2               0                 1
  RX               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     6
  XQ LOSS WILD-TYPE                                1    30
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           1    15
  XQ LOSS WILD-TYPE                         7    94
D80V10, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                30
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                         15                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"
D80V11, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1  17
  XQ LOSS WILD-TYPE   2 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   17
  XQ LOSS WILD-TYPE    2  126
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              17               126
[1] 2 2
[1] FALSE
