[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/15082975/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/15089886/transformed.cor.cli.txt"

nPatients in clinical file=363, in cluster file=370, common to both=357
[1]  82 357
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               303 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               303 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              215               142 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              215               142 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               44               313 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               44               313 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               40               317 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               40               317 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               35               322 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               35               322 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               38               319 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               38               319 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               26               331 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               26               331 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               350 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               350 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              132               225 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              132               225 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              104               253 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              104               253 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              111               246 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              111               246 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               62               295 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               62               295 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              107               250 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              107               250 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              107               250 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              107               250 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               75               282 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               75               282 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              182               175 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              182               175 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               18               339 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               18               339 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               337 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               337 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                60                297 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                60                297 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                36                321 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                36                321 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                340 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                340 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                18                339 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                18                339 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                39                318 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                39                318 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                44                313 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                44                313 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                335 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                335 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                23                334 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                23                334 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                324 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                324 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                28                329 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                28                329 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                14                343 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                14                343 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                30                327 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                30                327 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                92                265 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                92                265 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                35                322 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                35                322 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                27                330 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                27                330 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                53                304 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                53                304 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                68                289 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                68                289 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               105                252 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               105                252 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               109                248 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               109                248 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                331 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                331 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                48                309 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                48                309 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               39               318 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               39               318 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               61               296 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               61               296 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               81               276 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               81               276 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               335 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               335 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               31               326 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               31               326 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               36               321 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               36               321 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               50               307 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               50               307 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               38               319 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               38               319 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              102               255 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              102               255 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              142               215 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              142               215 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               27               330 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               27               330 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               38               319 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               38               319 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               27               330 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               27               330 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               90               267 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               90               267 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               15               342 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               15               342 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               20               337 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               20               337 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              185               172 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              185               172 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               42               315 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               42               315 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              115               242 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              115               242 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              105               252 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              105               252 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                44                313 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                44                313 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                74                283 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                74                283 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                61                296 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                61                296 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                70                287 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                70                287 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                60                297 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                60                297 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                33                324 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                33                324 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               115                242 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               115                242 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               104                253 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               104                253 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                63                294 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                63                294 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               108                249 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               108                249 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               143                214 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               143                214 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               177                180 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               177                180 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                37                320 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                37                320 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                70                287 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                70                287 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                73                284 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                73                284 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                53                304 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                53                304 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                38                319 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                38                319 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                333 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                333 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                12                345 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                12                345 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               106                251 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               106                251 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                66                291 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                66                291 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               92               265 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               92               265 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               68               289 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               68               289 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 357 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=104,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=223,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=10,	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:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 357 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"            "NEOPLASM_DISEASESTAGE"    
 [3] "PATHOLOGY_T_STAGE"         "PATHOLOGY_N_STAGE"        
 [5] "PATHOLOGY_M_STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL_TYPE"         "COMPLETENESS_OF_RESECTION"
 [9] "RACE"                      "ETHNICITY"                
YEARS_TO_BIRTH, nv=61, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1 178  91  73  12 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
  179    91    73    12 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1 178  91  73  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
  179    91    73    12 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
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    32  14
  1P GAIN WILD-TYPE 193  95
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               46               288 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               14                95 
$`1P GAIN MUTATED`
TCGA-2Y-A9GX TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10U 
       80.28        40.41        56.91         0.66        37.32        27.52 
TCGA-BC-A10W TCGA-BC-A216 TCGA-BW-A5NO TCGA-CC-5262 TCGA-DD-A114 TCGA-DD-A11A 
        2.99        44.42         0.66         3.39        37.78         2.60 
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-AACB TCGA-DD-AACJ 
       45.11         5.62        26.83        30.51        76.41        69.11 
TCGA-DD-AACL TCGA-DD-AACO TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AADL 
        3.52        61.68        21.63        44.22        40.47        20.91 
TCGA-DD-AADR TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAVW TCGA-DD-AAW1 TCGA-ED-A459 
       66.67        21.17        21.83        76.18        65.39        13.41 
TCGA-ED-A4XI TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A26S TCGA-G3-A25W 
       12.69         0.20        14.04         1.84        19.99        30.74 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV3 
       25.25        22.95        12.03         1.84        11.80         9.17 
TCGA-KR-A7K7 TCGA-RC-A7SH TCGA-UB-A7MF TCGA-UB-AA0U 
       13.38        15.39         7.04        10.75 

$`1P GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        41.79        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       27.88       120.82        41.33        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       37.25        20.81        14.99         1.18         8.55        13.02 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
        8.61        10.78        10.59        11.97        11.08         1.51 
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-BC-A8YO TCGA-BD-A2L6 
       22.36        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       13.45        36.66         0.07         2.86         3.19         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-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         7.33         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       11.47        12.95        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        27.19        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        90.28 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.97        30.15        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
       13.48         0.53        11.41        75.65        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK 
       63.48        12.00        15.42         6.41        53.19         0.30 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       58.16        42.81        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
        4.50        18.54        42.58        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.83        13.97        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       14.33        15.58        18.21        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       23.74        18.90        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        72.39        56.48        64.77        62.47        66.25 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       49.48        53.69        15.85        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20        12.82        13.15        13.41        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        20.61        19.59         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38        12.03         0.03         0.33        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.39        13.68        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-AAUZ 
       19.23        20.42        17.10         7.76         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
        8.55         9.70         0.89         8.75         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG 
       16.83         3.72         2.14        11.84        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.97        12.03         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         0.62        10.85        58.88        19.92        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK 
       21.01         3.09        21.04        19.33        19.04        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       24.13         0.76        17.59        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       15.98        10.32        11.34         0.99        12.99        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       13.55        35.77        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        40.80        79.30        11.21 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.20              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            80.28            120.82 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            21.40             18.97 
[1] "0.2 - 80.3 (21.4)"  "0.0 - 120.8 (19.0)"
[1] "hr=" "1"  
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P GAIN MUTATED        21       13         0         12          3          2
  1P GAIN WILD-TYPE     147       71         3         47          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P GAIN MUTATED          0         0         0
  1P GAIN WILD-TYPE        3         1         2
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 21               147
  STAGE II                13                71
  STAGE III                0                 3
  STAGE IIIA              12                47
  STAGE IIIB               3                 5
  STAGE IIIC               2                 5
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1P GAIN MUTATED      21  15  14   4
  1P GAIN WILD-TYPE   158  76  59   8
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1              21               158
  T2                 15                76
  T3                 14                59
  T4                  4                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    37   0
  1P GAIN WILD-TYPE 212   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     37    0
  1P GAIN WILD-TYPE  212    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              37               212
  1               0                 3
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    41   0
  1P GAIN WILD-TYPE 219   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     41    0
  1P GAIN WILD-TYPE  219    4
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              41               219
  1               0                 4
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    13  41
  1P GAIN WILD-TYPE 100 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     13   41
  1P GAIN WILD-TYPE  100  203
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              13               100
  MALE                41               203
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1P GAIN MUTATED                         0                       53
  1P GAIN WILD-TYPE                       2                      295
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1P GAIN MUTATED                                  1
  1P GAIN WILD-TYPE                                6
D1V8, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      53               295
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    45   5   0   2
  1P GAIN WILD-TYPE 270  10   1  17
D1V9, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              45               270
  R1               5                10
  R2               0                 1
  RX               2                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0    32
  1P GAIN WILD-TYPE                                1   124
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           3    19
  1P GAIN WILD-TYPE                        14   154
D1V10, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         32               124
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         19               154
[1] 4 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  52
  1P GAIN WILD-TYPE  11 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   52
  1P GAIN WILD-TYPE   11  277
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              52               277
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   138  62
  1Q GAIN WILD-TYPE  87  47
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              200               134 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               62                47 
$`1Q GAIN MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       63.75        41.79        80.28       120.82        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 
       41.33        37.25        20.81        14.99         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-BC-A10Q TCGA-BC-A10R 
       10.78        10.59         0.66        11.97        37.32        10.13 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG 
       27.52         2.99        23.34         5.03        44.42        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72        36.66         0.66         3.19         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        11.47 
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-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A7 
       27.19         5.62        19.76        25.81        17.59        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
        0.36        30.61        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73D 
       39.78        29.56        73.81        12.26         0.30        22.78 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC 
      114.35        13.48         0.53        11.41        76.41        55.40 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM 
       63.48        12.00        53.19        69.11         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       51.52         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD 
       42.58        44.22        40.08        40.54        13.97        40.47 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 
       14.89        15.06        66.67        18.21        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15         4.64        21.17        21.83        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.08        23.64        25.78        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       59.93        76.18        64.77        62.47        66.25        65.39 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       53.69        13.41        12.69        13.35         9.73        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
        0.20        14.04        13.15         1.84        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-FV-A2QQ TCGA-FV-A2QR 
       20.61        19.59         0.62         9.96        23.97        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X 
        8.12        12.03         0.03        13.68        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53        22.13        19.53        19.23        25.25 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.42        17.10        12.03         1.84         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ 
        9.70         9.17         8.75         2.14         3.02         2.99 
TCGA-HP-A5N0 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC 
       37.91         2.14        11.84        13.38        12.72        13.97 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-O8-A75V 
        9.57        16.67        18.38        12.85        20.71        17.69 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        24.13         0.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV 
       15.98         7.04        11.34         0.99        12.99        35.77 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CG 
       40.80        11.21 

$`1Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H4 
       23.80        53.39        83.24        24.89        27.88        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9HA TCGA-4R-AA8I TCGA-5R-AA1D TCGA-5R-AAAM 
       18.25        11.74         1.18         8.61        11.08         1.51 
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-BC-A8YO TCGA-BD-A2L6 
       69.57        13.84         0.26        17.98        18.48        44.81 
TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
       13.45         0.07         2.86         4.24         3.32         0.10 
TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A1EB TCGA-DD-A1EC 
        0.10        83.57        53.33         0.46        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A2 
       75.65         6.02        33.04        55.69         7.66        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       20.12       102.74       107.11        33.14        32.52        90.28 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       56.25       108.76        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACG 
       23.05         1.45        35.67        75.65        12.53        15.42 
TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD6 
        6.41         0.30        50.33        46.82         5.62        22.09 
TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS 
       40.83        39.52         3.78        29.52        14.33        15.58 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAEA 
       18.87        19.30        20.98        18.61        19.99        18.90 
TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAW2 
       16.37        50.33        35.08        72.39        56.48        49.48 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
       15.85        13.91         0.20        13.41        13.35         0.20 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 
       11.93        22.85        14.40        60.89        27.88         6.38 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33        81.73         0.39        51.06        53.79        28.27 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-AAUZ 
       25.64         5.92        22.95         7.76         5.98        11.24 
TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        0.89         1.02         2.20        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
        3.72        24.36        12.03         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       19.92        21.01         3.09        21.04        19.33        19.04 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WX-AA46 TCGA-YA-A8S7 
       17.59        19.76        10.75        10.32        24.85        13.55 
TCGA-ZP-A9CY TCGA-ZS-A9CF 
       25.71        79.30 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           120.82            108.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           18.920            19.545 
[1] "0.0 - 120.8 (18.9)" "0.1 - 108.8 (19.5)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED        98       55         2         29          6          3
  1Q GAIN WILD-TYPE      70       29         1         30          2          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q GAIN MUTATED          2         1         2
  1Q GAIN WILD-TYPE        1         0         0
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 98                70
  STAGE II                55                29
  STAGE III                2                 1
  STAGE IIIA              29                30
  STAGE IIIB               6                 2
  STAGE IIIC               3                 4
  STAGE IV                 2                 1
  STAGE IVA                1                 0
  STAGE IVB                2                 0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1Q GAIN MUTATED     106  59  40   8
  1Q GAIN WILD-TYPE    73  32  33   4
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1             106                73
  T2                 59                32
  T3                 40                33
  T4                  8                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   154   1
  1Q GAIN WILD-TYPE  95   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    154    1
  1Q GAIN WILD-TYPE   95    2
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             154                95
  1               1                 2
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   161   4
  1Q GAIN WILD-TYPE  99   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    161    4
  1Q GAIN WILD-TYPE   99    0
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             161                99
  1               4                 0
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    65 150
  1Q GAIN WILD-TYPE  48  94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     65  150
  1Q GAIN WILD-TYPE   48   94
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              65                48
  MALE               150                94
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1Q GAIN MUTATED                         0                      212
  1Q GAIN WILD-TYPE                       2                      136
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1Q GAIN MUTATED                                  3
  1Q GAIN WILD-TYPE                                4
D2V8, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     212               136
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED   194   8   1   9
  1Q GAIN WILD-TYPE 121   7   0  10
D2V9, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             194               121
  R1               8                 7
  R2               1                 0
  RX               9                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 GAIN MUTATED                                  1   103
  1Q GAIN WILD-TYPE                                0    53
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          11    94
  1Q GAIN WILD-TYPE                         6    79
D2V10, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                        103                53
  BLACK OR AFRICAN AMERICAN                     11                 6
  WHITE                                         94                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"
D2V11, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     6 200
  1Q GAIN WILD-TYPE   5 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6  200
  1Q GAIN WILD-TYPE    5  129
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 5
  NOT HISPANIC OR LATINO             200               129
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    20  19
  2P GAIN WILD-TYPE 205  90
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               39               295 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               19                90 
$`2P GAIN MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-5R-AA1C 
       63.75        24.89        27.88        56.91        18.25        11.97 
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        17.98         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        33.04        13.64        55.69 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AACB 
       30.61        33.14        22.78         1.45        13.48        76.41 
TCGA-DD-AACI TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADO TCGA-DD-AAVW TCGA-ED-A7PY 
       53.19         5.62        22.09        14.89        76.18        12.82 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z 
       13.41         1.84        22.85        51.06        30.74        21.53 
TCGA-LG-A6GG TCGA-UB-A7MA TCGA-YA-A8S7 
       12.72        17.59        13.55 

$`2P GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 
       23.80        53.39        83.24        41.79        80.28       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 
       40.41        41.33        47.74        11.74        37.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG 
       14.99         1.18         8.55        13.02         8.61        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10S 
       10.59         0.66        11.08         1.51        27.91        46.78 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        5.03        44.42        13.84         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       12.72        18.48        44.81        13.45        36.66         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.19         3.39         4.24         3.32 
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        11.47        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y 
       49.15         6.02        18.35        21.14        27.19         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        90.28 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G 
       78.84        23.93         9.30        23.05        35.67       114.35 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        75.65        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
        4.50        18.54        21.63        42.58        44.22        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       29.52        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.87        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       18.90        15.72        25.08        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       72.39        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         9.73         0.20         0.20        14.04        13.15 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.35         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62         9.96        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.33        81.73         0.39        13.68        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        25.25        22.95        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       12.03         5.98         1.84        11.24         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
        9.70         9.17         0.89         8.75         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83         3.72         2.14        11.84        13.38        24.36 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.97        12.03         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         0.62        10.85        58.88        19.92        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       21.01         3.09        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13         0.76        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.98         7.04        10.75        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       12.99        24.85        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.10              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            90.71            120.82 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            22.85             18.90 
[1] "0.1 - 90.7 (22.9)"  "0.0 - 120.8 (18.9)"
[1] "hr=" "1.4"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P GAIN MUTATED        14       11         0         11          1          2
  2P GAIN WILD-TYPE     154       73         3         48          7          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P GAIN MUTATED          1         0         1
  2P GAIN WILD-TYPE        2         1         1
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 14               154
  STAGE II                11                73
  STAGE III                0                 3
  STAGE IIIA              11                48
  STAGE IIIB               1                 7
  STAGE IIIC               2                 5
  STAGE IV                 1                 2
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2P GAIN MUTATED      15  14  13   2
  2P GAIN WILD-TYPE   164  77  60  10
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1              15               164
  T2                 14                77
  T3                 13                60
  T4                  2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    30   2
  2P GAIN WILD-TYPE 219   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     30    2
  2P GAIN WILD-TYPE  219    1
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              30               219
  1               2                 1
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    30   2
  2P GAIN WILD-TYPE 230   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     30    2
  2P GAIN WILD-TYPE  230    2
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              30               230
  1               2                 2
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    26  18
  2P GAIN WILD-TYPE  87 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     26   18
  2P GAIN WILD-TYPE   87  226
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              26                87
  MALE                18               226
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2P GAIN MUTATED                         0                       42
  2P GAIN WILD-TYPE                       2                      306
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2P GAIN MUTATED                                  2
  2P GAIN WILD-TYPE                                5
D3V8, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      42               306
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    38   5   0   1
  2P GAIN WILD-TYPE 277  10   1  18
D3V9, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              38               277
  R1               5                10
  R2               0                 1
  RX               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0    15
  2P GAIN WILD-TYPE                                1   141
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           1    28
  2P GAIN WILD-TYPE                        16   145
D3V10, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15               141
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         28               145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2  42
  2P GAIN WILD-TYPE   9 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   42
  2P GAIN WILD-TYPE    9  287
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              42               287
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    18  17
  2Q GAIN WILD-TYPE 207  92
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               35               299 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               17                92 
$`2Q GAIN MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H5 TCGA-5R-AA1C TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R 
       24.89        18.25        11.97        48.99        37.32        10.13 
TCGA-DD-A113 TCGA-DD-A1E9 TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 
       79.73        90.71        33.04        13.64        55.69        30.61 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AACU 
       22.78         1.45        13.48        76.41        53.19        51.52 
TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADO TCGA-DD-AADU TCGA-DD-AAVW TCGA-ED-A7PY 
        5.62        22.09        14.89        18.21        76.18        12.82 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W 
       13.41         1.84        22.85        13.68        51.06        30.74 
TCGA-G3-A25Z TCGA-G3-AAV6 TCGA-LG-A6GG TCGA-UB-A7MA TCGA-YA-A8S7 
       21.53         2.14        12.72        17.59        13.55 

$`2Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        37.25        20.81        14.99         1.18         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D 
       13.02         8.61        10.78        10.59         0.66        11.08 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
        1.51        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        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       18.48        44.81        13.45        36.66         0.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.19         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        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       45.11        49.15         6.02        18.35        21.14        27.19 
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-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        90.28        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
       35.67       114.35         0.53        11.41        75.65        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ 
       12.53        63.48        12.00        15.42         6.41        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.35        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
       47.67         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.87        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       18.90        15.72        25.08        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       72.39        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         9.73         0.20         0.20        14.04        13.15 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.35         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62         9.96        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.33        81.73         0.39        53.79        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        5.98         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.17         0.89         8.75         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        11.84        13.38        24.36        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
        9.57        16.67        18.38        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        19.92        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
        0.76        19.76        16.44         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       10.75        10.32        11.34         0.99        12.99        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        40.80        79.30        11.21 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.45              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            90.71            120.82 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            21.53             19.23 
[1] "1.4 - 90.7 (21.5)"  "0.0 - 120.8 (19.2)"
[1] "hr=" "1.5"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q GAIN MUTATED        13       11         0         10          1          1
  2Q GAIN WILD-TYPE     155       73         3         49          7          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q GAIN MUTATED          1         0         1
  2Q GAIN WILD-TYPE        2         1         1
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 13               155
  STAGE II                11                73
  STAGE III                0                 3
  STAGE IIIA              10                49
  STAGE IIIB               1                 7
  STAGE IIIC               1                 6
  STAGE IV                 1                 2
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2Q GAIN MUTATED      14  13  12   1
  2Q GAIN WILD-TYPE   165  78  61  11
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              14               165
  T2                 13                78
  T3                 12                61
  T4                  1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    31   1
  2Q GAIN WILD-TYPE 218   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     31    1
  2Q GAIN WILD-TYPE  218    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              31               218
  1               1                 2
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    30   2
  2Q GAIN WILD-TYPE 230   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     30    2
  2Q GAIN WILD-TYPE  230    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              30               230
  1               2                 2
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    23  17
  2Q GAIN WILD-TYPE  90 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     23   17
  2Q GAIN WILD-TYPE   90  227
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              23                90
  MALE                17               227
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2Q GAIN MUTATED                         0                       38
  2Q GAIN WILD-TYPE                       2                      310
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2Q GAIN MUTATED                                  2
  2Q GAIN WILD-TYPE                                5
D4V8, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      38               310
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    35   4   0   1
  2Q GAIN WILD-TYPE 280  11   1  18
D4V9, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              35               280
  R1               4                11
  R2               0                 1
  RX               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0    16
  2Q GAIN WILD-TYPE                                1   140
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           1    23
  2Q GAIN WILD-TYPE                        16   150
D4V10, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         16               140
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         23               150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2  38
  2Q GAIN WILD-TYPE   9 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   38
  2Q GAIN WILD-TYPE    9  291
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              38               291
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    21   9
  3P GAIN WILD-TYPE 204 100
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               30               304 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                9               100 
$`3P GAIN MUTATED`
TCGA-2Y-A9GS TCGA-5R-AA1C TCGA-BC-A217 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-A3M9 
       23.80        11.97        13.84        14.60         0.66         0.10 
TCGA-DD-A114 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NV 
       37.78        21.76        12.95        33.04         5.62        78.84 
TCGA-DD-A73E TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN 
        1.45         5.62        22.09        40.47        20.91        29.52 
TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEE TCGA-ED-A8O6 
       66.67        18.21         4.64        23.74        16.37         1.84 
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-AAV2 TCGA-MI-A75G TCGA-NI-A8LF TCGA-UB-A7ME 
       22.85         6.38         9.70        18.38        19.92        15.98 

$`3P GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        8.55        13.02         8.61        10.78        10.59         0.66 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       11.08         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER 
       17.98        12.72        18.48        44.81        13.45        36.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.19         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        11.47        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       49.15         6.02        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        90.28        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        80.75        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       22.78        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
        4.50        18.54        21.63        42.58        44.22        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.54        40.83        13.97        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       35.67        35.05        34.49         0.39        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       14.33        15.58        18.87        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.15        20.98        18.61        19.99        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       18.90        15.72        25.08        23.64        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41        13.35         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       20.61        19.59         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 
       60.89        23.97        19.10        27.88         8.12        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        81.73         0.39        13.68        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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24         8.55        11.80         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14         3.02         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.91        20.75        17.06        16.83         3.72         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       11.84        13.38        24.36        12.72        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.04        15.39        15.52        24.13         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       19.76        16.44         1.71         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       11.34         0.99        12.99        24.85        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            78.84            120.82 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            17.29             19.43 
[1] "0.1 - 78.8 (17.3)"  "0.0 - 120.8 (19.4)"
[1] "hr=" "1.3"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P GAIN MUTATED        18        8         0          6          0          1
  3P GAIN WILD-TYPE     150       76         3         53          8          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P GAIN MUTATED          2         0         0
  3P GAIN WILD-TYPE        1         1         2
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 18               150
  STAGE II                 8                76
  STAGE III                0                 3
  STAGE IIIA               6                53
  STAGE IIIB               0                 8
  STAGE IIIC               1                 6
  STAGE IV                 2                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3P GAIN MUTATED      19  10   6   0
  3P GAIN WILD-TYPE   160  81  67  12
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1              19               160
  T2                 10                81
  T3                  6                67
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    22   1
  3P GAIN WILD-TYPE 227   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     22    1
  3P GAIN WILD-TYPE  227    2
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              22               227
  1               1                 2
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    26   1
  3P GAIN WILD-TYPE 234   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     26    1
  3P GAIN WILD-TYPE  234    3
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              26               234
  1               1                 3
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     7  28
  3P GAIN WILD-TYPE 106 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      7   28
  3P GAIN WILD-TYPE  106  216
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               7               106
  MALE                28               216
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3P GAIN MUTATED                         0                       35
  3P GAIN WILD-TYPE                       2                      313
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3P GAIN MUTATED                                  0
  3P GAIN WILD-TYPE                                7
D5V8, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      35               313
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of 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    31   0   0   4
  3P GAIN WILD-TYPE 284  15   1  15
D5V9, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              31               284
  R1               0                15
  R2               0                 1
  RX               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0    17
  3P GAIN WILD-TYPE                                1   139
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           2    16
  3P GAIN WILD-TYPE                        15   157
D5V10, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17               139
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         16               157
[1] 4 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     2  32
  3P GAIN WILD-TYPE   9 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   32
  3P GAIN WILD-TYPE    9  297
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              32               297
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    21  12
  3Q GAIN WILD-TYPE 204  97
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               33               301 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               12                97 
$`3Q GAIN MUTATED`
TCGA-2Y-A9GS TCGA-5C-AAPD TCGA-5R-AA1C TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A69H 
       23.80         0.66        11.97        10.13        13.84        14.60 
TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EJ 
        0.66         0.10        37.78        21.76        12.95        33.04 
TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-AACL TCGA-DD-AACZ TCGA-DD-AADD 
        5.62        78.84         1.45         3.52         5.62        40.47 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE6 TCGA-DD-AAE9 
       20.91        29.52        66.67        18.21         4.64        23.74 
TCGA-DD-AAEE TCGA-DD-AAVS TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A7M9 TCGA-LG-A9QD 
       16.37        59.93        22.85         6.38         1.84        12.03 
TCGA-MI-A75G TCGA-NI-A8LF TCGA-UB-A7MD 
       18.38        19.92         1.71 

$`3Q GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1D 
        8.55        13.02         8.61        10.78        10.59        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T 
        1.51        48.99        27.91        37.32        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        17.98        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 
       18.48        44.81        13.45        36.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        3.19         3.39         4.24         3.32         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        79.73        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        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        11.47        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       18.35        13.64        21.14        27.19        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 
       90.28        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       80.75        23.93         9.30        23.05        22.78        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       53.19        69.11         0.30        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       13.97        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
       34.49         0.39        14.89        15.06        14.33        15.58 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.87        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB 
       18.61        19.99        21.17        21.83        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       89.69        82.62        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        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         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62         9.96        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10        27.88         8.12        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       81.73         0.39        13.68        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        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       17.10         7.76        12.03         5.98        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80         9.70         9.17         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83         3.72         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       24.36        12.72        13.97         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       20.71         0.62        10.85        58.88        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        3.09        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME 
       24.13         0.76        17.59        19.76        16.44        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        7.04        10.75        10.32        11.34         0.99        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        13.55        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            78.84            120.82 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            14.60             19.59 
[1] "0.1 - 78.8 (14.6)"  "0.0 - 120.8 (19.6)"
[1] "hr=" "1.6"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q GAIN MUTATED        19        9         0          5          1          1
  3Q GAIN WILD-TYPE     149       75         3         54          7          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q GAIN MUTATED          2         0         0
  3Q GAIN WILD-TYPE        1         1         2
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 19               149
  STAGE II                 9                75
  STAGE III                0                 3
  STAGE IIIA               5                54
  STAGE IIIB               1                 7
  STAGE IIIC               1                 6
  STAGE IV                 2                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3Q GAIN MUTATED      20  11   7   0
  3Q GAIN WILD-TYPE   159  80  66  12
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              20               159
  T2                 11                80
  T3                  7                66
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    24   1
  3Q GAIN WILD-TYPE 225   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     24    1
  3Q GAIN WILD-TYPE  225    2
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              24               225
  1               1                 2
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    27   1
  3Q GAIN WILD-TYPE 233   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     27    1
  3Q GAIN WILD-TYPE  233    3
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              27               233
  1               1                 3
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     8  30
  3Q GAIN WILD-TYPE 105 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8   30
  3Q GAIN WILD-TYPE  105  214
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               8               105
  MALE                30               214
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3Q GAIN MUTATED                         0                       37
  3Q GAIN WILD-TYPE                       2                      311
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3Q GAIN MUTATED                                  1
  3Q GAIN WILD-TYPE                                6
D6V8, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      37               311
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    34   0   0   4
  3Q GAIN WILD-TYPE 281  15   1  15
D6V9, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              34               281
  R1               0                15
  R2               0                 1
  RX               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  0    17
  3Q GAIN WILD-TYPE                                1   139
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                           3    18
  3Q GAIN WILD-TYPE                        14   155
D6V10, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17               139
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         18               155
[1] 4 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     3  34
  3Q GAIN WILD-TYPE   8 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   34
  3Q GAIN WILD-TYPE    8  295
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              34               295
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    21   3
  4P GAIN WILD-TYPE 204 106
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               24               310 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               106 
$`4P GAIN MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9H2 TCGA-2Y-A9H6 TCGA-2Y-A9H8 TCGA-BC-A10R TCGA-CC-5261 
       63.75        56.91        11.74        20.81        10.13         3.19 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A1EC TCGA-DD-A1EH 
        0.10         0.10       113.00         2.60        19.79        49.15 
TCGA-DD-A73G TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AADB TCGA-DD-AADO TCGA-DD-AAVS 
      114.35        53.19        58.16        40.83        14.89        59.93 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-G3-A3CG TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-WQ-A9G7 
       13.41        13.35        22.13        12.72         0.76         0.99 

$`4P GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       27.88       120.82        40.41        41.33        47.74        18.25 
TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       37.25        14.99         1.18         8.55        13.02         8.61 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        11.97        11.08         1.51 
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        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       12.72        18.48        44.81        13.45        36.66         0.66 
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-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-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-A1EI TCGA-DD-A1EJ 
       75.65        11.47        12.95        45.11         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        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        90.28        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       22.78         1.45        35.67        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN 
       15.42         6.41        69.11         0.30         3.52        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.54        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV 
       15.06        14.33        66.67        15.58        18.21        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
       19.99         4.64        21.17        21.83        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW 
       35.08        79.07        89.69        82.62        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
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        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        81.73         0.39        13.68        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        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14         3.02         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.91        20.75        17.06        16.83         3.72         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.84        13.38        24.36        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        19.92        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        24.13        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       19.76        16.44         1.71        15.98         7.04        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       10.32        11.34        12.99        24.85        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.10              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           114.35            120.82 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           17.340            19.265 
[1] "0.1 - 114.3 (17.3)" "0.0 - 120.8 (19.3)"
[1] "hr=" "3.4"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P GAIN MUTATED        10        7         1          5          0          0
  4P GAIN WILD-TYPE     158       77         2         54          8          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P GAIN MUTATED          0         0         0
  4P GAIN WILD-TYPE        3         1         2
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 10               158
  STAGE II                 7                77
  STAGE III                1                 2
  STAGE IIIA               5                54
  STAGE IIIB               0                 8
  STAGE IIIC               0                 7
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4P GAIN MUTATED      12   6   8   0
  4P GAIN WILD-TYPE   167  85  65  12
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1              12               167
  T2                  6                85
  T3                  8                65
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    19   0
  4P GAIN WILD-TYPE 230   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     19    0
  4P GAIN WILD-TYPE  230    3
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              19               230
  1               0                 3
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    21   0
  4P GAIN WILD-TYPE 239   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     21    0
  4P GAIN WILD-TYPE  239    4
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              21               239
  1               0                 4
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    12  14
  4P GAIN WILD-TYPE 101 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     12   14
  4P GAIN WILD-TYPE  101  230
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              12               101
  MALE                14               230
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4P GAIN MUTATED                         0                       26
  4P GAIN WILD-TYPE                       2                      322
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4P GAIN MUTATED                                  0
  4P GAIN WILD-TYPE                                7
D7V8, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      26               322
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of 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    23   1   0   2
  4P GAIN WILD-TYPE 292  14   1  17
D7V9, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              23               292
  R1               1                14
  R2               0                 1
  RX               2                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0    12
  4P GAIN WILD-TYPE                                1   144
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1    13
  4P GAIN WILD-TYPE                        16   160
D7V10, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         12               144
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         13               160
[1] 4 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  26
  4P GAIN WILD-TYPE  11 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   26
  4P GAIN WILD-TYPE   11  303
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              26               303
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     5   1
  4Q GAIN WILD-TYPE 220 108
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               328 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1               108 
$`4Q GAIN MUTATED`
TCGA-CC-5261 TCGA-DD-A1EC TCGA-DD-AACI TCGA-ED-A82E TCGA-G3-A3CG TCGA-G3-AAUZ 
        3.19        19.79        53.19        13.41        22.13        11.24 

$`4Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
        0.66        11.97        11.08         1.51        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       37.32        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       18.48        44.81        13.45        36.66         0.66         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-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       90.71        79.40        66.31        75.65        11.47        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        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       21.14        27.19        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        90.28 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
        6.41        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       18.21        18.87        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       20.98        18.61        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       23.74        18.90        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        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         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        14.04        13.15        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       81.73         0.39        13.68        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        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 
        7.76        12.03         5.98         1.84         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
        9.70         9.17         0.89         8.75         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83         3.72         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85        20.71         0.62        10.85        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       15.39        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       16.44         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       11.34         0.99        12.99        24.85        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3.19              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            53.19            120.82 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           16.600            19.265 
[1] "3.2 - 53.2 (16.6)"  "0.0 - 120.8 (19.3)"
[1] "hr=" "1.5"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q GAIN MUTATED         3        3         0          1          0          0
  4Q GAIN WILD-TYPE     165       81         3         58          8          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q GAIN MUTATED          0         0         0
  4Q GAIN WILD-TYPE        3         1         2
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  3               165
  STAGE II                 3                81
  STAGE III                0                 3
  STAGE IIIA               1                58
  STAGE IIIB               0                 8
  STAGE IIIC               0                 7
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4Q GAIN MUTATED       3   3   1   0
  4Q GAIN WILD-TYPE   176  88  72  12
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               3               176
  T2                  3                88
  T3                  1                72
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7   0
  4Q GAIN WILD-TYPE 242   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    0
  4Q GAIN WILD-TYPE  242    3
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               7               242
  1               0                 3
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7   0
  4Q GAIN WILD-TYPE 253   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    0
  4Q GAIN WILD-TYPE  253    4
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               7               253
  1               0                 4
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     2   5
  4Q GAIN WILD-TYPE 111 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    5
  4Q GAIN WILD-TYPE  111  239
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2               111
  MALE                 5               239
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4Q GAIN MUTATED                         0                        7
  4Q GAIN WILD-TYPE                       2                      341
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4Q GAIN MUTATED                                  0
  4Q GAIN WILD-TYPE                                7
D8V8, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                       7               341
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     5   1   0   1
  4Q GAIN WILD-TYPE 310  14   1  18
D8V9, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               5               310
  R1               1                14
  R2               0                 1
  RX               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     4
  4Q GAIN WILD-TYPE                                1   152
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     2
  4Q GAIN WILD-TYPE                        17   171
D8V10, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4               152
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                          2               171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   6
  4Q GAIN WILD-TYPE  10 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    6
  4Q GAIN WILD-TYPE   10  323
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO               6               323
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    73  48
  5P GAIN WILD-TYPE 152  61
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              121               213 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               48                61 
$`5P GAIN MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       41.79        24.89        27.88        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       47.74        20.81        14.99         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 
       10.78        37.32        10.13         2.99         5.03        13.84 
TCGA-BC-A3KG TCGA-BD-A3EP TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC 
       22.36        13.45         4.24         3.32         0.10         0.13 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       83.57        53.33       113.00        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       66.31        11.47        12.95        21.14        55.69         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND 
        7.66        17.59       102.74        13.78         0.36        90.28 
TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       39.78        73.81        78.84       114.35        13.48         0.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACV 
       12.00        15.42        53.19        69.11        13.64        50.33 
TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADF 
        5.62        21.63        44.22        40.08        13.97         3.78 
TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE3 
       29.52        14.33        66.67        18.21        18.25        18.61 
TCGA-DD-AAEA TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVY TCGA-DD-AAW0 
       18.90        16.37        23.64        35.08        64.77        66.25 
TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A7XP 
       49.48        13.41        13.35         9.73        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT 
       13.41         1.84        19.59         0.62         9.96        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
       19.10        27.88         0.03        81.73         0.39        51.06 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-AAV1 
       30.74        58.49        22.13        25.25        17.10        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K8 
        9.70         8.75         2.20         2.99        11.84        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.72        13.97        18.38        20.71        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-A7MF 
       17.69        21.01        19.04        24.13        15.98         7.04 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       10.75         0.99        12.99        23.21         0.69        24.43 
TCGA-ZS-A9CE 
       40.80 

$`5P GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9H0 
       23.80        53.39        63.75        83.24        80.28       120.82 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD 
       18.25        11.74        37.25         8.61        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
       11.97        11.08         1.51        48.99        27.91        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52        27.52        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       44.42         0.26        17.98        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       44.81        36.66         0.66         0.07         2.86         3.19 
TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 
        3.39         0.10         0.07        79.73        37.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG 
        2.60         0.46        21.76        19.79        75.65        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W 
       49.15         6.02        33.04        18.35        13.64        27.19 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 
       19.76        25.81        70.06        20.12       107.11        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        30.97        30.15        26.83        30.51 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56       108.76        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        63.48 
TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.35        51.52        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA 
       47.67         4.50        18.54        42.58        22.09        40.54 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.83        40.47        39.52        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADS 
       34.49        20.91         0.39        14.89        15.06        15.58 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       18.87        19.30        18.25        18.15        20.98        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        21.17        21.83        23.74        15.72        25.08 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW3 
       72.39        76.18        56.48        62.47        65.39        53.69 
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        12.82         0.20 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK 
       13.35         0.20        18.74        19.99        20.61        11.93 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       22.85        60.89        23.97         8.12         6.38        12.03 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
        0.33        13.68        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       25.64         5.92        19.53        19.23        22.95        20.42 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-HP-A5N0 
        9.17         0.89         2.14         3.02         1.02        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       20.75        17.06        16.83         3.72         2.14        13.38 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        12.85         0.62        10.85 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 
        3.09        21.04        19.33        15.39        15.52         0.76 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L 
       17.59        19.76        16.44         1.71        10.32        11.34 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D4 
       24.85        13.55        35.77        25.71        23.57        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           114.35            120.82 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            18.25             19.79 
[1] "0.0 - 114.3 (18.2)" "0.1 - 120.8 (19.8)"
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P GAIN MUTATED        55       33         1         28          4          1
  5P GAIN WILD-TYPE     113       51         2         31          4          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P GAIN MUTATED          1         0         0
  5P GAIN WILD-TYPE        2         1         2
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 55               113
  STAGE II                33                51
  STAGE III                1                 2
  STAGE IIIA              28                31
  STAGE IIIB               4                 4
  STAGE IIIC               1                 6
  STAGE IV                 1                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5P GAIN MUTATED      58  36  35   3
  5P GAIN WILD-TYPE   121  55  38   9
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1              58               121
  T2                 36                55
  T3                 35                38
  T4                  3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    88   0
  5P GAIN WILD-TYPE 161   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     88    0
  5P GAIN WILD-TYPE  161    3
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              88               161
  1               0                 3
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    95   1
  5P GAIN WILD-TYPE 165   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     95    1
  5P GAIN WILD-TYPE  165    3
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              95               165
  1               1                 3
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    40  92
  5P GAIN WILD-TYPE  73 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     40   92
  5P GAIN WILD-TYPE   73  152
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              40                73
  MALE                92               152
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5P GAIN MUTATED                         0                      129
  5P GAIN WILD-TYPE                       2                      219
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5P GAIN MUTATED                                  3
  5P GAIN WILD-TYPE                                4
D9V8, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     129               219
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED   117   6   0   6
  5P GAIN WILD-TYPE 198   9   1  13
D9V9, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0             117               198
  R1               6                 9
  R2               0                 1
  RX               6                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0    57
  5P GAIN WILD-TYPE                                1    99
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           7    61
  5P GAIN WILD-TYPE                        10   112
D9V10, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         57                99
  BLACK OR AFRICAN AMERICAN                      7                10
  WHITE                                         61               112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     4 120
  5P GAIN WILD-TYPE   7 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4  120
  5P GAIN WILD-TYPE    7  209
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 7
  NOT HISPANIC OR LATINO             120               209
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    59  37
  5Q GAIN WILD-TYPE 166  72
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               96               238 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               37                72 
$`5Q GAIN MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       41.79        24.89        27.88        40.41        41.33        47.74 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Q 
       14.99         1.18         8.55        13.02        10.78        37.32 
TCGA-BC-A10W TCGA-BC-A112 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A116 TCGA-DD-A118 
        2.99         5.03         0.10         0.13        53.33       113.00 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39X 
       51.29        90.71        79.40        11.47        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 
        5.62         7.66        17.59       102.74        13.78         0.36 
TCGA-DD-A4ND TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73G 
       90.28        39.78        73.81        78.84        23.93       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI 
       13.48         0.53        55.40        12.00        15.42        53.19 
TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AADC 
       69.11        13.64        50.33         5.62        21.63        13.97 
TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU 
        3.78         0.39        29.52        14.33        66.67        18.21 
TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVX 
       18.25        18.61        18.90        23.64        35.08        56.48 
TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7XO 
       64.77        66.25        49.48        13.41         9.73        14.04 
TCGA-ED-A7XP TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A495 
       13.15        19.59         0.62         9.96        14.40         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A5SM TCGA-G3-AAV1 
        0.39        51.06        30.74        22.13        17.10        11.80 
TCGA-G3-AAV5 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-LG-A9QC 
        8.75         2.20         2.99        11.84        12.72        13.97 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF TCGA-RG-A7D4 
       18.38        20.71        19.92        17.69        19.04        24.13 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
        0.99        12.99        23.21         0.69        24.43        40.80 

$`5Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9H0 
       23.80        53.39        63.75        83.24        80.28       120.82 
TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-4R-AA8I 
       56.91        18.25        11.74        37.25        20.81         8.61 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.59         0.66        11.97        11.08         1.51        48.99 
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-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       22.36        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.45        36.66         0.66         0.07         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 
        3.39         4.24         3.32         0.10         0.07        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       37.78        83.57         7.33         2.60         0.46        21.76 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39Z 
        6.02        33.04        18.35        13.64        27.19        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        30.97        30.15        26.83        30.51        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73B 
       29.56       108.76        12.26         0.30        80.75         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACA 
       23.05        22.78         1.45        35.67        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL 
       76.41        12.53        63.48         6.41         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       58.16        42.81        61.68        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 
       51.52        46.82         5.59        47.67         4.50        18.54 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW 
       20.91        14.89        15.06        15.58        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        18.15        20.98        19.99         4.64        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
       21.83        23.74        15.72        25.08        16.37        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       76.18        62.47        65.39        53.69        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        12.82         0.20        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        60.89        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        8.12         6.38        12.03         0.33        81.73        13.68 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       53.79        28.27        58.49        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        25.25        22.95        20.42 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.70         9.17         0.89         2.14         3.02         1.02 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.91        20.75        17.06        16.83         3.72         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       13.38        24.36        12.03         9.57        16.67        12.85 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
        0.62        10.85        58.88        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.33        15.39        15.52         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       16.44         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
       11.34        24.85        13.55        35.77        25.71        23.57 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           114.35            120.82 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           18.315            19.760 
[1] "0.0 - 114.3 (18.3)" "0.1 - 120.8 (19.8)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q GAIN MUTATED        46       28         1         16          3          1
  5Q GAIN WILD-TYPE     122       56         2         43          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q GAIN MUTATED          1         0         0
  5Q GAIN WILD-TYPE        2         1         2
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 46               122
  STAGE II                28                56
  STAGE III                1                 2
  STAGE IIIA              16                43
  STAGE IIIB               3                 5
  STAGE IIIC               1                 6
  STAGE IV                 1                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5Q GAIN MUTATED      48  32  22   2
  5Q GAIN WILD-TYPE   131  59  51  10
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1              48               131
  T2                 32                59
  T3                 22                51
  T4                  2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    69   0
  5Q GAIN WILD-TYPE 180   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     69    0
  5Q GAIN WILD-TYPE  180    3
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              69               180
  1               0                 3
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    74   1
  5Q GAIN WILD-TYPE 186   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     74    1
  5Q GAIN WILD-TYPE  186    3
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              74               186
  1               1                 3
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    26  78
  5Q GAIN WILD-TYPE  87 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     26   78
  5Q GAIN WILD-TYPE   87  166
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              26                87
  MALE                78               166
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5Q GAIN MUTATED                         0                      102
  5Q GAIN WILD-TYPE                       2                      246
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5Q GAIN MUTATED                                  2
  5Q GAIN WILD-TYPE                                5
D10V8, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     102               246
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    95   4   0   4
  5Q GAIN WILD-TYPE 220  11   1  15
D10V9, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              95               220
  R1               4                11
  R2               0                 1
  RX               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0    46
  5Q GAIN WILD-TYPE                                1   110
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           6    47
  5Q GAIN WILD-TYPE                        11   126
D10V10, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         46               110
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         47               126
[1] 4 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     4  96
  5Q GAIN WILD-TYPE   7 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4   96
  5Q GAIN WILD-TYPE    7  233
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 7
  NOT HISPANIC OR LATINO              96               233
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    66  34
  6P GAIN WILD-TYPE 159  75
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              100               234 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               34                75 
$`6P GAIN MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       23.80        24.89        27.88        41.33        18.25        20.81 
TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5R-AA1C TCGA-BC-A10U 
        1.18        13.02         8.61        10.78        11.97        27.52 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       13.84        22.36        14.60        44.81        13.45         0.66 
TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH 
        4.24         0.13        37.78         7.33        45.11        49.15 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NN TCGA-DD-A4NS 
       55.69         5.62         0.36        30.61        29.56        80.75 
TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB 
        9.30        22.78         1.45         0.53        75.65        76.41 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACN 
       12.53        63.48        12.00        53.19        69.11        42.81 
TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADG TCGA-DD-AADL 
       13.64        51.35        42.58        40.54        37.64        20.91 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADV TCGA-DD-AAE0 TCGA-DD-AAE3 
       29.52        14.89        14.33        18.87        18.25        18.61 
TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       23.74        25.78        35.08        82.62        59.93        76.18 
TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E 
       64.77        49.48        53.69        13.35         0.20        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 
       13.35         1.84        19.59         0.62        22.85        27.88 
TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CK 
        6.38        13.68        53.79        58.49        22.13        19.23 
TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 
       25.25        20.42         7.76        11.80         9.17         0.89 
TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF 
       11.84        12.72        18.38        12.85        20.71        19.92 
TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF 
       21.04        15.52        24.13        17.59        16.44         7.04 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CD 
       10.75         0.99        13.55        45.57 

$`6P GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 
       53.39        63.75        83.24        41.79        80.28       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 
       40.41        56.91        47.74        11.74        37.25        14.99 
TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55        10.59         0.66        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W 
       27.91        37.32        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 
        0.26        17.98        12.72        18.48        36.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.19         3.39         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.10        79.73        83.57        53.33       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        11.47        12.95         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        27.19        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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78        33.14        32.52        90.28        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       26.83        30.51        39.78        56.25        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73F 
       12.26         0.30        78.84        23.93        23.05        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH 
      114.35        13.48        11.41        55.40        15.42         6.41 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS 
        0.30         3.52        58.16        61.68        14.20        59.31 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        21.63        44.22        22.09        40.08 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADI 
       40.83        13.97        40.47        39.52         3.78        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS 
       35.05        34.49         0.39        15.06        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       18.21        19.30        18.25        18.15        20.98        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        21.17        21.83        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVU 
       16.37        23.64        50.33        79.07        89.69        72.39 
TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A4XI 
       56.48        62.47        66.25        65.39        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       15.85        13.91         9.73         0.20        12.82        14.04 
TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
       13.15         0.20        18.74        19.99        20.61         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       11.93        14.40        60.89        23.97        19.10         8.12 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
       12.03         0.03         0.33        81.73         0.39        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        30.74        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       19.53        22.95        17.10        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.24         8.55         9.70         8.75         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       16.83         3.72         2.14        13.38        24.36        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       12.03         9.57        16.67         0.62        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       17.69        21.01         3.09        19.33        19.04        15.39 
TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L 
        0.76        19.76         1.71        15.98        10.32        11.34 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       12.99        24.85        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
        0.69        24.43        12.99        40.80        79.30        11.21 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.13              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            82.62            120.82 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            19.41             19.20 
[1] "0.1 - 82.6 (19.4)"  "0.0 - 120.8 (19.2)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P GAIN MUTATED        46       31         1         21          3          1
  6P GAIN WILD-TYPE     122       53         2         38          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P GAIN MUTATED          2         0         1
  6P GAIN WILD-TYPE        1         1         1
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 46               122
  STAGE II                31                53
  STAGE III                1                 2
  STAGE IIIA              21                38
  STAGE IIIB               3                 5
  STAGE IIIC               1                 6
  STAGE IV                 2                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6P GAIN MUTATED      47  34  26   3
  6P GAIN WILD-TYPE   132  57  47   9
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1              47               132
  T2                 34                57
  T3                 26                47
  T4                  3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    77   0
  6P GAIN WILD-TYPE 172   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     77    0
  6P GAIN WILD-TYPE  172    3
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              77               172
  1               0                 3
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    82   2
  6P GAIN WILD-TYPE 178   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     82    2
  6P GAIN WILD-TYPE  178    2
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              82               178
  1               2                 2
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    31  80
  6P GAIN WILD-TYPE  82 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     31   80
  6P GAIN WILD-TYPE   82  164
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              31                82
  MALE                80               164
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6P GAIN MUTATED                         0                      108
  6P GAIN WILD-TYPE                       2                      240
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6P GAIN MUTATED                                  3
  6P GAIN WILD-TYPE                                4
D11V8, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     108               240
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED   100   5   1   5
  6P GAIN WILD-TYPE 215  10   0  14
D11V9, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0             100               215
  R1               5                10
  R2               1                 0
  RX               5                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0    56
  6P GAIN WILD-TYPE                                1   100
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           7    48
  6P GAIN WILD-TYPE                        10   125
D11V10, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         56               100
  BLACK OR AFRICAN AMERICAN                      7                10
  WHITE                                         48               125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     4 104
  6P GAIN WILD-TYPE   7 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4  104
  6P GAIN WILD-TYPE    7  225
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 7
  NOT HISPANIC OR LATINO             104               225
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    34  20
  6Q GAIN WILD-TYPE 191  89
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               54               280 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               20                89 
$`6Q GAIN MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9HA TCGA-3K-AAZ8 
       23.80        24.89        41.33        18.25         1.18        13.02 
TCGA-5C-A9VG TCGA-BC-A3KG TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5263 
       10.78        22.36        14.60        44.81        13.45         4.24 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39Y 
        0.13        37.78         7.33        45.11        49.15         5.62 
TCGA-DD-A3A9 TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACJ 
       30.61         9.30        22.78        76.41        12.53        69.11 
TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AAE0 
       42.81        51.35        29.52        14.89        14.33        18.25 
TCGA-DD-AAE3 TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAW2 TCGA-ED-A66X TCGA-EP-A2KB 
       18.61        25.78        35.08        49.48        13.35        19.59 
TCGA-EP-A2KC TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SI 
        0.62        13.68        53.79        22.13        19.23        25.25 
TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H TCGA-RC-A7S9 
       11.80        11.84        12.72        18.38        12.85        21.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MF TCGA-YA-A8S7 TCGA-ZS-A9CD 
       15.52        24.13        16.44         7.04        13.55        45.57 

$`6Q GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
      120.82        40.41        56.91        47.74        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD 
       20.81        14.99         8.55         8.61        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       11.97        11.08         1.51        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO 
        0.26        17.98        12.72        18.48        36.66         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         2.86         3.19         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10        79.73        83.57        53.33       113.00 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI 
       66.31        19.79        75.65        11.47        12.95         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        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 
       90.28        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       80.75        78.84        23.93        23.05         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
      114.35        13.48         0.53        11.41        75.65        55.40 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK 
       63.48        12.00        15.42         6.41        53.19         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        3.52        58.16        61.68        13.64        14.20        59.31 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV 
        0.39        15.06        66.67        15.58        18.21        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       19.30        18.25        18.15        20.98        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       21.17        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       16.37        23.64        50.33        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        53.69        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.91         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        20.61         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       60.89        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
       12.03         0.03         0.33        81.73         0.39        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       28.27        30.74        58.49        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
        5.92        19.53        22.95        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       12.03         5.98         1.84        11.24         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.17         0.89         8.75         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.91        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
        3.72         2.14        13.38        24.36        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF 
       19.92        17.69        21.01         3.09        19.33        19.04 
TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       15.39         0.76        17.59        19.76         1.71        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       10.75        10.32        11.34         0.99        12.99        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        40.80        79.30        11.21 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.13              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            76.41            120.82 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           18.495            19.430 
[1] "0.1 - 76.4 (18.5)"  "0.0 - 120.8 (19.4)"
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q GAIN MUTATED        24       16         1         13          2          1
  6Q GAIN WILD-TYPE     144       68         2         46          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q GAIN MUTATED          2         0         1
  6Q GAIN WILD-TYPE        1         1         1
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 24               144
  STAGE II                16                68
  STAGE III                1                 2
  STAGE IIIA              13                46
  STAGE IIIB               2                 6
  STAGE IIIC               1                 6
  STAGE IV                 2                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6Q GAIN MUTATED      24  18  16   3
  6Q GAIN WILD-TYPE   155  73  57   9
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1              24               155
  T2                 18                73
  T3                 16                57
  T4                  3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    44   0
  6Q GAIN WILD-TYPE 205   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     44    0
  6Q GAIN WILD-TYPE  205    3
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              44               205
  1               0                 3
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    43   2
  6Q GAIN WILD-TYPE 217   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     43    2
  6Q GAIN WILD-TYPE  217    2
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              43               217
  1               2                 2
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    15  47
  6Q GAIN WILD-TYPE  98 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     15   47
  6Q GAIN WILD-TYPE   98  197
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              15                98
  MALE                47               197
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6Q GAIN MUTATED                         0                       61
  6Q GAIN WILD-TYPE                       2                      287
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6Q GAIN MUTATED                                  1
  6Q GAIN WILD-TYPE                                6
D12V8, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      61               287
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    55   2   1   4
  6Q GAIN WILD-TYPE 260  13   0  15
D12V9, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              55               260
  R1               2                13
  R2               1                 0
  RX               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0    31
  6Q GAIN WILD-TYPE                                1   125
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           5    26
  6Q GAIN WILD-TYPE                        12   147
D12V10, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         31               125
  BLACK OR AFRICAN AMERICAN                      5                12
  WHITE                                         26               147
[1] 4 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     4  56
  6Q GAIN WILD-TYPE   7 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4   56
  6Q GAIN WILD-TYPE    7  273
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 7
  NOT HISPANIC OR LATINO              56               273
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    63  34
  7P GAIN WILD-TYPE 162  75
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               97               237 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               34                75 
$`7P GAIN MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 
       23.80        63.75        41.79        24.89        27.88        56.91 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
       20.81        14.99        13.02         8.61        10.78        10.59 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 
       37.32        10.13        27.52        13.45         0.66         2.86 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1E9 
        0.10        79.73       113.00         2.60        51.29        90.71 
TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       19.79        11.47        33.04        21.14         5.62        19.76 
TCGA-DD-A3A2 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NK 
       70.06        13.78        33.14        90.28        26.83        39.78 
TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AACD 
       12.26        78.84        22.78         1.45       114.35        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACZ 
       63.48        12.00        53.19        13.64        51.35         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADS TCGA-DD-AAE0 
        4.50        42.58        40.47        20.91        15.58        18.25 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAVP 
       18.61         4.64        23.74        18.90        15.72        79.07 
TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       64.77        49.48        53.69         9.73         0.20        12.82 
TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 
       14.04         1.84         0.62         9.96        22.85         6.38 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X 
        0.33        81.73        13.68        51.06        28.27        58.49 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-AAV1 
       22.13        19.53        20.42        17.10         7.76        11.80 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A8LF 
        8.75         2.14        11.84        12.72        18.38        19.92 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
       15.98        10.75         0.99        12.99        24.85        13.55 
TCGA-ZP-A9D1 
        0.69 

$`7P GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 
       53.39        83.24        80.28       120.82        40.41        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        11.74        37.25         1.18         8.55 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
        0.66        11.97        11.08         1.51        48.99        27.91 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       69.57         5.03        44.42        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER 
       17.98        14.60        12.72        18.48        44.81        36.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         3.19         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        0.07         0.13        37.78        83.57        53.33         7.33 
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-A39W 
       45.11        49.15         6.02        18.35        13.64        27.19 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       55.69        25.81         7.66        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      107.11         0.36        30.61        32.52        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR 
       30.51        56.25        29.56        73.81       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-AA3A 
       80.75        23.93         9.30        23.05        35.67        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG 
        0.53        11.41        75.65        76.41        55.40        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
        6.41        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       61.68        14.20        59.31        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.59        47.67        18.54        21.63        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF 
       40.08        40.54        40.83        13.97        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN 
       37.64        35.67        35.05        34.49         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADV 
       14.89        15.06        14.33        66.67        18.21        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 
       19.30        18.25        18.15        20.98        19.99        21.17 
TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       21.83        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       35.08        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A4XI 
       56.48        62.47        66.25        65.39        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        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.35         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25W 
        8.12        12.03         0.03         0.39        53.79        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53        25.64         5.92        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       22.95        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.70         9.17         0.89         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        13.38        24.36        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        12.85        20.71         0.62        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       15.39        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-ZP-A9CV 
       16.44         1.71         7.04        10.32        11.34        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.10              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           114.35            120.82 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            18.38             19.59 
[1] "0.1 - 114.3 (18.4)" "0.0 - 120.8 (19.6)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED        47       26         0         19          4          4
  7P GAIN WILD-TYPE     121       58         3         40          4          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P GAIN MUTATED          2         0         0
  7P GAIN WILD-TYPE        1         1         2
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 47               121
  STAGE II                26                58
  STAGE III                0                 3
  STAGE IIIA              19                40
  STAGE IIIB               4                 4
  STAGE IIIC               4                 3
  STAGE IV                 2                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7P GAIN MUTATED      50  30  24   3
  7P GAIN WILD-TYPE   129  61  49   9
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              50               129
  T2                 30                61
  T3                 24                49
  T4                  3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    69   2
  7P GAIN WILD-TYPE 180   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     69    2
  7P GAIN WILD-TYPE  180    1
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              69               180
  1               2                 1
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    79   1
  7P GAIN WILD-TYPE 181   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     79    1
  7P GAIN WILD-TYPE  181    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              79               181
  1               1                 3
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    39  68
  7P GAIN WILD-TYPE  74 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     39   68
  7P GAIN WILD-TYPE   74  176
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              39                74
  MALE                68               176
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7P GAIN MUTATED                         0                      106
  7P GAIN WILD-TYPE                       2                      242
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7P GAIN MUTATED                                  1
  7P GAIN WILD-TYPE                                6
D13V8, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     106               242
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED    94   6   0   6
  7P GAIN WILD-TYPE 221   9   1  13
D13V9, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              94               221
  R1               6                 9
  R2               0                 1
  RX               6                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1    41
  7P GAIN WILD-TYPE                                0   115
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           5    58
  7P GAIN WILD-TYPE                        12   115
D13V10, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         41               115
  BLACK OR AFRICAN AMERICAN                      5                12
  WHITE                                         58               115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     4 100
  7P GAIN WILD-TYPE   7 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4  100
  7P GAIN WILD-TYPE    7  229
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 7
  NOT HISPANIC OR LATINO             100               229
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    62  35
  7Q GAIN WILD-TYPE 163  74
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               97               237 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               35                74 
$`7Q GAIN MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 
       23.80        63.75        41.79        24.89        27.88        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG 
       41.33        20.81        14.99        13.02         8.61        10.78 
TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A5W4 TCGA-BD-A3EP 
       10.59        37.32        10.13        27.52        17.98        13.45 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A 
        0.66         2.86         0.10         0.10       113.00         2.60 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A39V 
       51.29        90.71        19.79        11.47        33.04        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NI 
        5.62        19.76        70.06        33.14        90.28        26.83 
TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73G 
       39.78        12.26        78.84        23.05         1.45       114.35 
TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACP 
       75.65        12.53        63.48        12.00        53.19        13.64 
TCGA-DD-AACT TCGA-DD-AADD TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADS 
       51.35        40.47        37.64        20.91         0.39        15.58 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEI 
       18.61         4.64        23.74        18.90        15.72        50.33 
TCGA-DD-AAVX TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PY 
       56.48        49.48        53.69        13.41         9.73        12.82 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       19.99        20.61         0.62         9.96        22.85         8.12 
TCGA-FV-A3R2 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ 
        6.38        51.06        28.27        58.49        22.13        19.53 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-G3-AAV6 
       20.42        17.10         7.76        11.80         8.75         2.14 
TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A7S9 
       11.84        12.72        18.38        58.88        19.92        21.04 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
        1.71        10.75         0.99        12.99        24.85        13.55 
TCGA-ZP-A9D1 
        0.69 

$`7Q GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 
       53.39        83.24        80.28       120.82        40.41        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-AAPD 
       18.25        11.74        37.25         1.18         8.55         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
       11.97        11.08         1.51        48.99        27.91        46.78 
TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        5.03        44.42        13.84         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5261 
       12.72        18.48        44.81        36.66         0.07         3.19 
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-A39W TCGA-DD-A39X TCGA-DD-A3A0 
        6.02        18.35        13.64        27.19        55.69        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
        0.36        30.61        32.52        30.97        30.15        30.51 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
       23.93         9.30        22.78        35.67        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ 
       11.41        76.41        55.40        15.42         6.41        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ 
        0.30         3.52        58.16        42.81        61.68        14.20 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       59.31        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE 
       22.09        40.08        40.54        40.83        13.97        39.52 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADN TCGA-DD-AADO 
        3.78        35.67        35.05        34.49        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       15.06        14.33        66.67        18.21        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 
       18.25        18.25        18.15        20.98        19.99        21.17 
TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
       21.83        25.08        16.37        23.64        25.78        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A4XI TCGA-ED-A5KG 
       64.77        62.47        66.25        65.39        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91        13.35         0.20         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KB 
       13.41        13.35         1.84         0.20        18.74        19.59 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
       12.03         0.03         0.33        81.73         0.39        13.68 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        30.74        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       19.23        25.25        22.95        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
       11.24         8.55         9.70         9.17         0.89         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       16.83         3.72         2.14        13.38        24.36        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF 
       10.85        17.69        21.01         3.09        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       15.39        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-ZP-A9CV 
       16.44        15.98         7.04        10.32        11.34        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.10              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           114.35            120.82 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            19.76             19.10 
[1] "0.1 - 114.3 (19.8)" "0.0 - 120.8 (19.1)"
[1] "hr=" "1.2"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED        45       28         0         20          3          4
  7Q GAIN WILD-TYPE     123       56         3         39          5          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q GAIN MUTATED          2         0         0
  7Q GAIN WILD-TYPE        1         1         2
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 45               123
  STAGE II                28                56
  STAGE III                0                 3
  STAGE IIIA              20                39
  STAGE IIIB               3                 5
  STAGE IIIC               4                 3
  STAGE IV                 2                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7Q GAIN MUTATED      48  32  24   3
  7Q GAIN WILD-TYPE   131  59  49   9
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              48               131
  T2                 32                59
  T3                 24                49
  T4                  3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    70   2
  7Q GAIN WILD-TYPE 179   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     70    2
  7Q GAIN WILD-TYPE  179    1
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              70               179
  1               2                 1
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    75   1
  7Q GAIN WILD-TYPE 185   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     75    1
  7Q GAIN WILD-TYPE  185    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              75               185
  1               1                 3
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    35  72
  7Q GAIN WILD-TYPE  78 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     35   72
  7Q GAIN WILD-TYPE   78  172
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              35                78
  MALE                72               172
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7Q GAIN MUTATED                         0                      106
  7Q GAIN WILD-TYPE                       2                      242
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7Q GAIN MUTATED                                  1
  7Q GAIN WILD-TYPE                                6
D14V8, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     106               242
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED    94   5   0   6
  7Q GAIN WILD-TYPE 221  10   1  13
D14V9, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              94               221
  R1               5                10
  R2               0                 1
  RX               6                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  1    39
  7Q GAIN WILD-TYPE                                0   117
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           6    60
  7Q GAIN WILD-TYPE                        11   113
D14V10, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         39               117
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         60               113
[1] 4 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     5 100
  7Q GAIN WILD-TYPE   6 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  100
  7Q GAIN WILD-TYPE    6  229
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 6
  NOT HISPANIC OR LATINO             100               229
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    50  19
  8P GAIN WILD-TYPE 175  90
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               69               265 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               19                90 
$`8P GAIN MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9H1 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1D TCGA-BC-4072 
       41.79        40.41        10.78        10.59        11.08        48.99 
TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A119 TCGA-DD-A11A 
       46.78         0.07         3.32         0.10         7.33         2.60 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A3A1 TCGA-DD-A4NN 
       90.71        19.79        12.95         6.02         7.66        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACI 
       73.81        12.26        80.75         0.53        12.53        53.19 
TCGA-DD-AACJ TCGA-DD-AACT TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 
       69.11        51.35         5.62        18.54        21.63        44.22 
TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADL TCGA-DD-AADR TCGA-DD-AADU 
       22.09        40.47        39.52        20.91        66.67        18.21 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVW TCGA-DD-AAVX 
       18.15        18.61        50.33        35.08        76.18        56.48 
TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XP TCGA-ED-A82E 
       49.48        13.41        13.35         9.73        13.15        13.41 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-FV-A4ZQ TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A5SJ 
       19.59         9.96         0.39        58.49        21.53        22.95 
TCGA-G3-A5SL TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-K7-AAU7 
       20.42         5.98        11.24        11.80         9.17         3.72 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75H TCGA-MR-A8JO TCGA-UB-A7MC 
       11.84        13.38        12.03        12.85        10.85        16.44 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZS-A9CD 
        0.99        12.99        45.57 

$`8P GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       27.88       120.82        56.91        41.33        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        37.25        20.81        14.99         1.18         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4073 
       13.02         8.61         0.66        11.97         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
        0.26        22.36        17.98        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 
       44.81        13.45        36.66         0.66         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        3.39         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-A1ED TCGA-DD-A1EE TCGA-DD-A1EG 
       51.29        79.40        66.31        75.65        11.47        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       49.15        33.04        18.35        13.64        21.14        27.19 
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        90.28        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NV 
       30.51        39.78        56.25       108.76         0.30        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      114.35        13.48        11.41        75.65        76.41        55.40 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL 
       63.48        12.00        15.42         6.41         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59        47.67         4.50 
TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF 
       42.58        40.08        40.54        40.83        13.97         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN 
       37.64        35.67        35.05        34.49         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW 
       14.89        15.06        14.33        15.58        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        18.25        20.98        19.99         4.64        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.83        23.74        18.90        15.72        25.08        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       23.64        25.78        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW3 
       72.39        64.77        62.47        66.25        65.39        53.69 
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        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       14.04        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       20.61         0.62        11.93        22.85        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33        81.73        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        30.74        14.86        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       19.53        19.23        25.25        17.10         7.76        12.03 
TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
        1.84         8.55         9.70         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       17.06        16.83         2.14        24.36        12.72        13.97 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 
        9.57        16.67        18.38        20.71         0.62        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       19.92        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.04        15.39        15.52        24.13         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       19.76         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       11.34        24.85        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57         0.69        24.43        12.99        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.07              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            90.71            120.82 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            16.44             19.76 
[1] "0.1 - 90.7 (16.4)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P GAIN MUTATED        37       17         0         15          1          1
  8P GAIN WILD-TYPE     131       67         3         44          7          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P GAIN MUTATED          1         0         0
  8P GAIN WILD-TYPE        2         1         2
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 37               131
  STAGE II                17                67
  STAGE III                0                 3
  STAGE IIIA              15                44
  STAGE IIIB               1                 7
  STAGE IIIC               1                 6
  STAGE IV                 1                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8P GAIN MUTATED      37  17  18   2
  8P GAIN WILD-TYPE   142  74  55  10
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              37               142
  T2                 17                74
  T3                 18                55
  T4                  2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    61   0
  8P GAIN WILD-TYPE 188   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     61    0
  8P GAIN WILD-TYPE  188    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              61               188
  1               0                 3
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    62   1
  8P GAIN WILD-TYPE 198   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     62    1
  8P GAIN WILD-TYPE  198    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              62               198
  1               1                 3
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    16  59
  8P GAIN WILD-TYPE  97 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     16   59
  8P GAIN WILD-TYPE   97  185
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              16                97
  MALE                59               185
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8P GAIN MUTATED                         1                       72
  8P GAIN WILD-TYPE                       1                      276
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8P GAIN MUTATED                                  2
  8P GAIN WILD-TYPE                                5
D15V8, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      72               276
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    65   2   1   5
  8P GAIN WILD-TYPE 250  13   0  14
D15V9, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              65               250
  R1               2                13
  R2               1                 0
  RX               5                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0    40
  8P GAIN WILD-TYPE                                1   116
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           1    32
  8P GAIN WILD-TYPE                        16   141
D15V10, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         40               116
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         32               141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3  68
  8P GAIN WILD-TYPE   8 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   68
  8P GAIN WILD-TYPE    8  261
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              68               261
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   116  51
  8Q GAIN WILD-TYPE 109  58
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              167               167 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               51                58 
$`8Q GAIN MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       41.79        24.89        40.41        56.91        47.74        18.25 
TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D 
        1.18        13.02        10.78        10.59        11.97        11.08 
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-BD-A3ER TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
       36.66         0.07         3.32         0.10         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
       79.73        53.33       113.00         7.33         2.60        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI 
       90.71        19.79        11.47        12.95        45.11         6.02 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 
       13.64        21.14         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        90.28        30.97        26.83        30.51        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        22.78       114.35 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACG 
        0.53        11.41        75.65        76.41        12.53        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41        53.19        69.11        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 
       13.64        51.35         5.62        18.54        21.63        44.22 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.67        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 
       14.33        66.67        18.21        18.25        18.15        18.61 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI 
       21.83        23.74        25.08        16.37        23.64        50.33 
TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       35.08        59.93        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66X 
       66.25        65.39        49.48        53.69        13.41        13.35 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A12J 
        9.73         0.20        13.15        13.41         1.84        18.74 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       20.61        19.59         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       14.40        23.97         8.12         6.38        81.73         0.39 
TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ 
       51.06        30.74        58.49        21.53        22.13        19.53 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       25.25        22.95        20.42        12.03         5.98        11.24 
TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-K7-AAU7 
       11.80         9.17         8.75         2.99        16.83         3.72 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       11.84        13.38        12.03         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
       20.71        10.85        17.69        19.04        15.39        24.13 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       16.44         1.71        15.98        10.75         0.99        12.99 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       13.55        35.77        12.99        45.57        11.21 

$`8Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       23.80        53.39        63.75        83.24        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H3 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
      120.82        41.33        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q 
        8.55         8.61         0.66         1.51        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       10.13        27.52        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-A69I 
        5.03        44.42        13.84        22.36        17.98        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 
       18.48        44.81        13.45         0.66         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B 
        3.39         4.24         0.07        37.78        83.57         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ 
       51.29        79.40        66.31        75.65        49.15        33.04 
TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 
       18.35        27.19        55.69        25.81        70.06        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NV TCGA-DD-A73A 
       30.15        39.78        56.25       108.76        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AACC 
        9.30        23.05         1.45        35.67        13.48        55.40 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACQ TCGA-DD-AACS 
       63.48        12.00         0.30         3.52        14.20        59.31 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59        47.67         4.50 
TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADP 
       42.58        40.08         3.78        37.64        35.05        15.06 
TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 
       15.58        18.87        19.30        18.25        20.98        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEH TCGA-DD-AAVP 
        4.64        21.17        18.90        15.72        25.78        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       89.69        82.62        72.39        12.69        15.85        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A26S 
        0.20        12.82        14.04        13.35         0.20        19.99 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       60.89        19.10        27.88        12.03         0.03         0.33 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI 
       13.68        53.79        28.27        14.86        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV2 
       19.23        17.10         7.76         1.84         8.55         9.70 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 
        0.89         2.14         3.02         1.02         2.20        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       20.75        17.06         2.14        24.36        12.72        13.97 
TCGA-MI-A75G TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
       18.38         0.62        58.88        19.92        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       21.04        19.33        15.52         0.76        17.59        19.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        7.04        10.32        11.34        24.85        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57         0.69        24.43        40.80        79.30 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           114.35            120.82 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            18.54             19.92 
[1] "0.1 - 114.3 (18.5)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED        84       49         0         33          3          2
  8Q GAIN WILD-TYPE      84       35         3         26          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q GAIN MUTATED          2         1         0
  8Q GAIN WILD-TYPE        1         0         2
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 84                84
  STAGE II                49                35
  STAGE III                0                 3
  STAGE IIIA              33                26
  STAGE IIIB               3                 5
  STAGE IIIC               2                 5
  STAGE IV                 2                 1
  STAGE IVA                1                 0
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  8Q GAIN MUTATED      87 52 38  4
  8Q GAIN WILD-TYPE    92 39 35  8
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              87                92
  T2                 52                39
  T3                 38                35
  T4                  4                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   135   1
  8Q GAIN WILD-TYPE 114   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    135    1
  8Q GAIN WILD-TYPE  114    2
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             135               114
  1               1                 2
[1] 2 2
[1] FALSE
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   137   2
  8Q GAIN WILD-TYPE 123   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    137    2
  8Q GAIN WILD-TYPE  123    2
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             137               123
  1               2                 2
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    43 139
  8Q GAIN WILD-TYPE  70 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     43  139
  8Q GAIN WILD-TYPE   70  105
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              43                70
  MALE               139               105
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8Q GAIN MUTATED                         1                      179
  8Q GAIN WILD-TYPE                       1                      169
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8Q GAIN MUTATED                                  2
  8Q GAIN WILD-TYPE                                5
D16V8, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                     179               169
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   161   8   1   9
  8Q GAIN WILD-TYPE 154   7   0  10
D16V9, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             161               154
  R1               8                 7
  R2               1                 0
  RX               9                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
  8Q GAIN MUTATED                                  1    90
  8Q GAIN WILD-TYPE                                0    66
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          10    76
  8Q GAIN WILD-TYPE                         7    97
D16V10, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         90                66
  BLACK OR AFRICAN AMERICAN                     10                 7
  WHITE                                         76                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"
D16V11, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     6 169
  8Q GAIN WILD-TYPE   5 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6  169
  8Q GAIN WILD-TYPE    5  160
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 5
  NOT HISPANIC OR LATINO             169               160
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    10   3
  9P GAIN WILD-TYPE 215 106
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               321 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               106 
$`9P GAIN MUTATED`
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-BW-A5NO TCGA-DD-A3A7 TCGA-DD-A4NV TCGA-DD-AACB 
        0.66        11.97         0.66        13.78        78.84        76.41 
TCGA-DD-AADJ TCGA-ED-A66Y TCGA-ED-A7XO TCGA-EP-A2KB TCGA-G3-A25U TCGA-KR-A7K2 
       35.05         9.73        14.04        19.59        53.79        11.84 
TCGA-ZP-A9D1 
        0.69 

$`9P GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       11.08         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       22.36        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45        36.66         0.07         2.86         3.19         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        11.47        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        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 
       70.06        17.59        20.12       102.74       107.11         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        90.28        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        75.65        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK 
       40.47        39.52         3.78        37.64        35.67        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       66.67        15.58        18.21        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       21.17        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       16.37        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
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-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       12.82         0.20        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        20.61         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
       81.73         0.39        13.68        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        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80         9.70         9.17         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83         3.72         2.14        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85        20.71         0.62        10.85        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       15.39        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       16.44         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       11.34         0.99        12.99        24.85        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.66              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            78.84            120.82 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            13.78             19.33 
[1] "0.7 - 78.8 (13.8)"  "0.0 - 120.8 (19.3)"
[1] "hr=" "1.2"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P GAIN MUTATED         5        3         0          7          1          0
  9P GAIN WILD-TYPE     163       81         3         52          7          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P GAIN MUTATED          1         0         0
  9P GAIN WILD-TYPE        2         1         2
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  5               163
  STAGE II                 3                81
  STAGE III                0                 3
  STAGE IIIA               7                52
  STAGE IIIB               1                 7
  STAGE IIIC               0                 7
  STAGE IV                 1                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9P GAIN MUTATED       6   4   8   0
  9P GAIN WILD-TYPE   173  87  65  12
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               6               173
  T2                  4                87
  T3                  8                65
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    15   0
  9P GAIN WILD-TYPE 234   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15    0
  9P GAIN WILD-TYPE  234    3
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              15               234
  1               0                 3
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    14   1
  9P GAIN WILD-TYPE 246   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     14    1
  9P GAIN WILD-TYPE  246    3
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              14               246
  1               1                 3
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     8  10
  9P GAIN WILD-TYPE 105 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      8   10
  9P GAIN WILD-TYPE  105  234
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               8               105
  MALE                10               234
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9P GAIN MUTATED                         0                       16
  9P GAIN WILD-TYPE                       2                      332
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9P GAIN MUTATED                                  2
  9P GAIN WILD-TYPE                                5
D17V8, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      16               332
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    15   0   0   3
  9P GAIN WILD-TYPE 300  15   1  16
D17V9, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              15               300
  R1               0                15
  R2               0                 1
  RX               3                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0    10
  9P GAIN WILD-TYPE                                1   146
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           1     6
  9P GAIN WILD-TYPE                        16   167
D17V10, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10               146
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                          6               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  15
  9P GAIN WILD-TYPE  10 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   15
  9P GAIN WILD-TYPE   10  314
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              15               314
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     9   4
  9Q GAIN WILD-TYPE 216 105
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               13               321 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               105 
$`9Q GAIN MUTATED`
TCGA-2Y-A9GY TCGA-5R-AA1C TCGA-BW-A5NO TCGA-DD-A3A6 TCGA-DD-A4NV TCGA-DD-AACY 
       24.89        11.97         0.66       107.11        78.84        47.67 
TCGA-DD-AADJ TCGA-ED-A66Y TCGA-EP-A2KB TCGA-G3-A25U TCGA-KR-A7K2 TCGA-WQ-A9G7 
       35.05         9.73        19.59        53.79        11.84         0.99 
TCGA-ZP-A9D1 
        0.69 

$`9Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        8.55        13.02         8.61        10.78        10.59         0.66 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       11.08         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       22.36        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45        36.66         0.07         2.86         3.19         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        11.47        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        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 
       70.06        17.59        20.12       102.74        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        90.28        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       63.48        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK 
       40.47        39.52         3.78        37.64        35.67        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       66.67        15.58        18.21        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       21.17        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       16.37        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        1.84         0.20        18.74        19.99        20.61         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        9.96        11.93        22.85        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
        0.33        81.73         0.39        13.68        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        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
        8.55        11.80         9.70         9.17         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       20.75        17.06        16.83         3.72         2.14        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       18.38        12.85        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       19.92        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.04        15.39        15.52        24.13         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       19.76        16.44         1.71        15.98         7.04        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       10.32        11.34        12.99        24.85        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.66              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           107.11            120.82 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            19.59             19.23 
[1] "0.7 - 107.1 (19.6)" "0.0 - 120.8 (19.2)"
[1] "hr=" "1.3"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q GAIN MUTATED         5        5         0          7          0          0
  9Q GAIN WILD-TYPE     163       79         3         52          8          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q GAIN MUTATED          1         0         0
  9Q GAIN WILD-TYPE        2         1         2
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  5               163
  STAGE II                 5                79
  STAGE III                0                 3
  STAGE IIIA               7                52
  STAGE IIIB               0                 8
  STAGE IIIC               0                 7
  STAGE IV                 1                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9Q GAIN MUTATED       6   6   8   0
  9Q GAIN WILD-TYPE   173  85  65  12
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               6               173
  T2                  6                85
  T3                  8                65
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    15   0
  9Q GAIN WILD-TYPE 234   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     15    0
  9Q GAIN WILD-TYPE  234    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              15               234
  1               0                 3
[1] 2 2
[1] FALSE
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    15   1
  9Q GAIN WILD-TYPE 245   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     15    1
  9Q GAIN WILD-TYPE  245    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              15               245
  1               1                 3
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    11   9
  9Q GAIN WILD-TYPE 102 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     11    9
  9Q GAIN WILD-TYPE  102  235
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              11               102
  MALE                 9               235
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9Q GAIN MUTATED                         0                       19
  9Q GAIN WILD-TYPE                       2                      329
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9Q GAIN MUTATED                                  1
  9Q GAIN WILD-TYPE                                6
D18V8, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      19               329
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    17   0   0   3
  9Q GAIN WILD-TYPE 298  15   1  16
D18V9, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              17               298
  R1               0                15
  R2               0                 1
  RX               3                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0    10
  9Q GAIN WILD-TYPE                                1   146
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           1     9
  9Q GAIN WILD-TYPE                        16   164
D18V10, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10               146
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                          9               164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  18
  9Q GAIN WILD-TYPE  10 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   18
  9Q GAIN WILD-TYPE   10  311
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              18               311
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    35  15
  10P GAIN WILD-TYPE 190  94
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                50                284 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                15                 94 
$`10P GAIN MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10R 
       23.80         1.18        13.02        10.78        37.32        10.13 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A1EL TCGA-DD-A3A9 
        0.10        79.73        37.78         2.60        13.64        30.61 
TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACM TCGA-DD-AACZ 
       78.84        22.78       114.35        76.41        58.16         5.62 
TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADV TCGA-DD-AADW 
       44.22        40.47         3.78        29.52        18.87        19.30 
TCGA-DD-AAE3 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAED TCGA-DD-AAEK TCGA-ED-A459 
       18.61        21.83        23.74        25.08        35.08        13.41 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-ES-A2HS 
       13.35         9.73        13.41         1.84        19.59        22.85 
TCGA-FV-A4ZQ TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-AAV5 TCGA-G3-AAV6 
        0.39        22.95        20.42        17.10         8.75         2.14 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7ME 
       10.85        19.92        15.39        15.52        17.59        15.98 
TCGA-UB-AA0U TCGA-YA-A8S7 
       10.75        13.55 

$`10P GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB 
       18.25        11.74        37.25        20.81        14.99         8.55 
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
        8.61        10.59         0.66        11.97        11.08         1.51 
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        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       18.48        44.81        13.45        36.66         0.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.19         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.07         0.13        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-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
        6.02        33.04        18.35        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        90.28        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E 
        0.30        80.75        23.93         9.30        23.05         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
       35.67        13.48         0.53        11.41        75.65        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       69.11         0.30         3.52        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59        47.67         4.50        18.54        21.63        42.58 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE 
       22.09        40.08        40.54        40.83        13.97        39.52 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.25        18.15        20.98        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       21.17        18.90        15.72        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
       49.48        53.69        12.69        15.85        13.91         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K 
       12.82         0.20        14.04        13.15        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        20.61         0.62         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        60.89        23.97        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        12.03         0.03         0.33        81.73        13.68 
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-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       25.25         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
        8.55        11.80         9.70         9.17         0.89         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83         3.72         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       12.85        20.71         0.62        58.88        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-T1-A6J8 
        3.09        21.04        19.33        19.04        24.13         0.76 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       19.76        16.44         1.71         7.04        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99        12.99        24.85        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.10               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            114.35             120.82 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            18.100             19.645 
[1] "0.1 - 114.3 (18.1)" "0.0 - 120.8 (19.6)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10P GAIN MUTATED        22       17         0         15          1
  10P GAIN WILD-TYPE     146       67         3         44          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P GAIN MUTATED            0        2         0         1
  10P GAIN WILD-TYPE          7        1         1         1
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  22                146
  STAGE II                 17                 67
  STAGE III                 0                  3
  STAGE IIIA               15                 44
  STAGE IIIB                1                  7
  STAGE IIIC                0                  7
  STAGE IV                  2                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10P GAIN MUTATED      22  20  17   1
  10P GAIN WILD-TYPE   157  71  56  11
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1               22                157
  T2                  20                 71
  T3                  17                 56
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    43   0
  10P GAIN WILD-TYPE 206   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     43    0
  10P GAIN WILD-TYPE  206    3
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               43                206
  1                0                  3
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    44   2
  10P GAIN WILD-TYPE 216   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     44    2
  10P GAIN WILD-TYPE  216    2
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               44                216
  1                2                  2
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    19  41
  10P GAIN WILD-TYPE  94 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     19   41
  10P GAIN WILD-TYPE   94  203
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               19                 94
  MALE                 41                203
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10P GAIN MUTATED                         1                       58
  10P GAIN WILD-TYPE                       1                      290
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10P GAIN MUTATED                                  1
  10P GAIN WILD-TYPE                                6
D19V8, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       58                290
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    53   3   0   4
  10P GAIN WILD-TYPE 262  12   1  15
D19V9, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               53                262
  R1                3                 12
  R2                0                  1
  RX                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0    32
  10P GAIN WILD-TYPE                                1   124
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           4    24
  10P GAIN WILD-TYPE                        13   149
D19V10, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          32                124
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          24                149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3  56
  10P GAIN WILD-TYPE   8 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3   56
  10P GAIN WILD-TYPE    8  273
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               56                273
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    22   7
  10Q GAIN WILD-TYPE 203 102
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                29                305 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                102 
$`10Q GAIN MUTATED`
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-DD-A113 TCGA-DD-A39Z TCGA-DD-A3A9 TCGA-DD-A4NV 
       13.02        10.78        79.73        19.76        30.61        78.84 
TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AADD TCGA-DD-AADN TCGA-DD-AADV TCGA-DD-AAE9 
      114.35        76.41        40.47        29.52        18.87        23.74 
TCGA-DD-AAED TCGA-DD-AAEK TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KB 
       25.08        35.08        13.35         9.73        13.41        19.59 
TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-AAV5 TCGA-G3-AAV6 
       22.85         0.39        20.42        17.10         8.75         2.14 
TCGA-NI-A8LF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-AA0U TCGA-YA-A8S7 
       19.92        15.39        17.59        10.75        13.55 

$`10Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        1.18         8.55         8.61        10.59         0.66        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       11.08         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       22.36        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.45        36.66         0.66         0.07         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        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        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        55.69         5.62        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        90.28        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        80.75        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       22.78         1.45        35.67        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       75.65        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF 
       40.08        40.54        40.83        13.97        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB 
       19.99         4.64        21.17        21.83        18.90        15.72 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        23.64        25.78        50.33        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        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        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       14.04        13.15        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       60.89        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33        81.73        13.68        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        25.25 
TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       22.95         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
        8.55        11.80         9.70         9.17         0.89         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83         3.72         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85        20.71         0.62        10.85        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK 
       21.01         3.09        21.04        19.33        19.04        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       24.13         0.76        19.76        16.44         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
        7.04        10.32        11.34         0.99        12.99        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        40.80        79.30        11.21 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.39               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            114.35             120.82 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             19.59              19.23 
[1] "0.4 - 114.3 (19.6)" "0.0 - 120.8 (19.2)"
[1] "hr=" "1.4"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q GAIN MUTATED        11       12         0         10          1
  10Q GAIN WILD-TYPE     157       72         3         49          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q GAIN MUTATED            0        1         0         1
  10Q GAIN WILD-TYPE          7        2         1         1
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  11                157
  STAGE II                 12                 72
  STAGE III                 0                  3
  STAGE IIIA               10                 49
  STAGE IIIB                1                  7
  STAGE IIIC                0                  7
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10Q GAIN MUTATED      11  13  11   1
  10Q GAIN WILD-TYPE   168  78  62  11
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1               11                168
  T2                  13                 78
  T3                  11                 62
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    26   0
  10Q GAIN WILD-TYPE 223   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     26    0
  10Q GAIN WILD-TYPE  223    3
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               26                223
  1                0                  3
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    27   2
  10Q GAIN WILD-TYPE 233   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     27    2
  10Q GAIN WILD-TYPE  233    2
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               27                233
  1                2                  2
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    14  22
  10Q GAIN WILD-TYPE  99 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     14   22
  10Q GAIN WILD-TYPE   99  222
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               14                 99
  MALE                 22                222
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10Q GAIN MUTATED                         0                       35
  10Q GAIN WILD-TYPE                       2                      313
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10Q GAIN MUTATED                                  1
  10Q GAIN WILD-TYPE                                6
D20V8, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       35                313
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    32   2   0   2
  10Q GAIN WILD-TYPE 283  13   1  17
D20V9, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               32                283
  R1                2                 13
  R2                0                  1
  RX                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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    17
  10Q GAIN WILD-TYPE                                1   139
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           1    17
  10Q GAIN WILD-TYPE                        16   156
D20V10, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          17                139
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                          17                156
[1] 4 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     2  33
  10Q GAIN WILD-TYPE   9 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   33
  10Q GAIN WILD-TYPE    9  296
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               33                296
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    10   4
  11P GAIN WILD-TYPE 215 105
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                14                320 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                105 
$`11P GAIN MUTATED`
TCGA-2Y-A9GZ TCGA-BC-A69H TCGA-BD-A3EP TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A4NV 
       27.88        14.60        13.45         7.33         5.62        78.84 
TCGA-DD-AAD1 TCGA-ED-A66Y TCGA-ED-A82E TCGA-FV-A4ZQ TCGA-G3-A3CG TCGA-LG-A6GG 
       18.54         9.73        13.41         0.39        22.13        12.72 
TCGA-UB-A7ME TCGA-WQ-A9G7 
       15.98         0.99 

$`11P GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       24.89       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        8.55        13.02         8.61        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       11.97        11.08         1.51        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
        0.26        22.36        17.98        12.72        18.48        44.81 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       36.66         0.66         0.07         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
       79.73        37.78        83.57        53.33       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        90.28        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        80.75        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
       47.67         5.62         4.50        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       66.67        15.58        18.21        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       21.17        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       16.37        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 
       12.82         0.20        14.04        13.15        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        9.96        11.93        22.85        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33        81.73        13.68        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        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80         9.70         9.17         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83         3.72         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       24.36        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85        20.71         0.62        10.85        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       15.39        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       16.44         1.71         7.04        10.75        10.32        11.34 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       12.99        24.85        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.39               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             78.84             120.82 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            13.430             19.675 
[1] "0.4 - 78.8 (13.4)"  "0.0 - 120.8 (19.7)"
[1] "hr=" "1.4"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P GAIN MUTATED         7        3         0          5          0
  11P GAIN WILD-TYPE     161       81         3         54          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P GAIN MUTATED            0        1         0         0
  11P GAIN WILD-TYPE          7        2         1         2
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   7                161
  STAGE II                  3                 81
  STAGE III                 0                  3
  STAGE IIIA                5                 54
  STAGE IIIB                0                  8
  STAGE IIIC                0                  7
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11P GAIN MUTATED       7   3   7   0
  11P GAIN WILD-TYPE   172  88  66  12
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                7                172
  T2                   3                 88
  T3                   7                 66
  T4                   0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     9   0
  11P GAIN WILD-TYPE 240   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      9    0
  11P GAIN WILD-TYPE  240    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                9                240
  1                0                  3
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    13   1
  11P GAIN WILD-TYPE 247   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     13    1
  11P GAIN WILD-TYPE  247    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               13                247
  1                1                  3
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     7  10
  11P GAIN WILD-TYPE 106 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7   10
  11P GAIN WILD-TYPE  106  234
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                7                106
  MALE                 10                234
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11P GAIN MUTATED                         0                       17
  11P GAIN WILD-TYPE                       2                      331
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11P GAIN MUTATED                                  0
  11P GAIN WILD-TYPE                                7
D21V8, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       17                331
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of 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    13   2   1   1
  11P GAIN WILD-TYPE 302  13   0  18
D21V9, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               13                302
  R1                2                 13
  R2                1                  0
  RX                1                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     8
  11P GAIN WILD-TYPE                                1   148
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           1     8
  11P GAIN WILD-TYPE                        16   165
D21V10, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                148
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           8                165
[1] 4 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  17
  11P GAIN WILD-TYPE  11 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   17
  11P GAIN WILD-TYPE   11  312
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               17                312
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    10   5
  11Q GAIN WILD-TYPE 215 104
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                319 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                104 
$`11Q GAIN MUTATED`
TCGA-2Y-A9GZ TCGA-BC-A69I TCGA-BD-A3EP TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A3A0 
       27.88        12.72        13.45         7.33         5.62        25.81 
TCGA-DD-A4NV TCGA-DD-AAD1 TCGA-DD-AADW TCGA-DD-AAE0 TCGA-ED-A66Y TCGA-ED-A82E 
       78.84        18.54        19.30        18.25         9.73        13.41 
TCGA-G3-A3CG TCGA-LG-A6GG TCGA-WQ-A9G7 
       22.13        12.72         0.99 

$`11Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       24.89       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        8.55        13.02         8.61        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       11.97        11.08         1.51        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 
        0.26        22.36        17.98        14.60        18.48        44.81 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       36.66         0.66         0.07         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
       79.73        37.78        83.57        53.33       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        90.28        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62         4.50        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
       15.58        18.21        18.87        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       18.90        15.72        25.08        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        49.48        53.69        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.91        13.35         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       20.61        19.59         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        60.89        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38        12.03         0.03         0.33        81.73         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       13.68        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        5.98         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.17         0.89         8.75         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.91        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
        3.72         2.14        11.84        13.38        24.36        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        0.62        10.85        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        3.09        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       24.13         0.76        17.59        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
       15.98         7.04        10.75        10.32        11.34        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        13.55        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.99               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             78.84             120.82 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.45              19.59 
[1] "1.0 - 78.8 (13.4)"  "0.0 - 120.8 (19.6)"
[1] "hr=" "1.5"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED         8        2         0          6          0
  11Q GAIN WILD-TYPE     160       82         3         53          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q GAIN MUTATED            0        1         0         0
  11Q GAIN WILD-TYPE          7        2         1         2
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   8                160
  STAGE II                  2                 82
  STAGE III                 0                  3
  STAGE IIIA                6                 53
  STAGE IIIB                0                  8
  STAGE IIIC                0                  7
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11Q GAIN MUTATED       8   2   8   0
  11Q GAIN WILD-TYPE   171  89  65  12
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                8                171
  T2                   2                 89
  T3                   8                 65
  T4                   0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    12   0
  11Q GAIN WILD-TYPE 237   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     12    0
  11Q GAIN WILD-TYPE  237    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               12                237
  1                0                  3
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    15   1
  11Q GAIN WILD-TYPE 245   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     15    1
  11Q GAIN WILD-TYPE  245    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               15                245
  1                1                  3
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     8  10
  11Q GAIN WILD-TYPE 105 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      8   10
  11Q GAIN WILD-TYPE  105  234
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                8                105
  MALE                 10                234
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11Q GAIN MUTATED                         0                       18
  11Q GAIN WILD-TYPE                       2                      330
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11Q GAIN MUTATED                                  0
  11Q GAIN WILD-TYPE                                7
D22V8, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       18                330
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of 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    14   2   1   1
  11Q GAIN WILD-TYPE 301  13   0  18
D22V9, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               14                301
  R1                2                 13
  R2                1                  0
  RX                1                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     9
  11Q GAIN WILD-TYPE                                1   147
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           1     8
  11Q GAIN WILD-TYPE                        16   165
D22V10, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                147
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           8                165
[1] 4 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  17
  11Q GAIN WILD-TYPE  11 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   17
  11Q GAIN WILD-TYPE   11  312
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               17                312
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    21  11
  12P GAIN WILD-TYPE 204  98
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                32                302 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                 98 
$`12P GAIN MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9H2 TCGA-5C-A9VG TCGA-BW-A5NO TCGA-DD-A11A TCGA-DD-A1EF 
       41.79        56.91        10.78         0.66         2.60        12.95 
TCGA-DD-A3A7 TCGA-DD-A4NR TCGA-DD-A73G TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACZ 
       13.78         0.30       114.35        53.19         0.30         5.62 
TCGA-DD-AADF TCGA-DD-AADR TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E 
        3.78        66.67         9.73         0.20         0.20        13.41 
TCGA-EP-A3JL TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 
        9.96        27.88        51.06         1.84        11.80         2.14 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75C TCGA-NI-A8LF TCGA-PD-A5DF TCGA-UB-A7MA 
        3.72        11.84         9.57        19.92        21.01        17.59 
TCGA-UB-A7ME TCGA-WQ-A9G7 
       15.98         0.99 

$`12P GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       27.88       120.82        40.41        41.33        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        37.25        20.81        14.99         1.18         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02         8.61        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        1.51        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       69.57         5.03        44.42        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       17.98        14.60        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       36.66         0.07         2.86         3.19         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-A1EJ 
       75.65        11.47        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        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 
       90.28        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76        12.26        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       35.67        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       69.11         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59        47.67         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       15.58        18.21        18.87        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.15        20.98        18.61        19.99         4.64        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.83        23.74        18.90        15.72        25.08        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       23.64        25.78        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO 
       12.69        15.85        13.91        13.35        12.82        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       20.61        19.59         0.62        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       60.89        23.97        19.10         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.03         0.33        81.73         0.39        13.68        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        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       20.42        17.10         7.76        12.03         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
        8.55         9.70         9.17         0.89         8.75         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       16.83         2.14        13.38        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03        16.67        18.38        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       10.85        58.88        17.69         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB 
       19.04        15.39        15.52        24.13         0.76        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       16.44         1.71         7.04        10.75        10.32        11.34 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       12.99        24.85        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.20               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            114.35             120.82 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             11.29              19.89 
[1] "0.2 - 114.3 (11.3)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1.5"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P GAIN MUTATED        15        8         0         11          3
  12P GAIN WILD-TYPE     153       76         3         48          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P GAIN MUTATED            1        0         0         0
  12P GAIN WILD-TYPE          6        3         1         2
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  15                153
  STAGE II                  8                 76
  STAGE III                 0                  3
  STAGE IIIA               11                 48
  STAGE IIIB                3                  5
  STAGE IIIC                1                  6
  STAGE IV                  0                  3
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12P GAIN MUTATED      15   8  14   2
  12P GAIN WILD-TYPE   164  83  59  10
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               15                164
  T2                   8                 83
  T3                  14                 59
  T4                   2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    29   0
  12P GAIN WILD-TYPE 220   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     29    0
  12P GAIN WILD-TYPE  220    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               29                220
  1                0                  3
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    31   0
  12P GAIN WILD-TYPE 229   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     31    0
  12P GAIN WILD-TYPE  229    4
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               31                229
  1                0                  4
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    16  23
  12P GAIN WILD-TYPE  97 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     16   23
  12P GAIN WILD-TYPE   97  221
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               16                 97
  MALE                 23                221
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12P GAIN MUTATED                         0                       35
  12P GAIN WILD-TYPE                       2                      313
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12P GAIN MUTATED                                  4
  12P GAIN WILD-TYPE                                3
D23V8, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       35                313
  HEPATOCHOLANGIOCARCINOMA (MIXED)                4                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    33   1   0   3
  12P GAIN WILD-TYPE 282  14   1  16
D23V9, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               33                282
  R1                1                 14
  R2                0                  1
  RX                3                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0    18
  12P GAIN WILD-TYPE                                1   138
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           2    18
  12P GAIN WILD-TYPE                        15   155
D23V10, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          18                138
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          18                155
[1] 4 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  37
  12P GAIN WILD-TYPE  11 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   37
  12P GAIN WILD-TYPE   11  292
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               37                292
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    26  11
  12Q GAIN WILD-TYPE 199  98
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                37                297 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                 98 
$`12Q GAIN MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-5C-A9VG TCGA-BC-A3KF TCGA-BW-A5NO 
       41.79       120.82        56.91        10.78         0.26         0.66 
TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A3A7 TCGA-DD-A4ND TCGA-DD-A4NH 
        2.60        12.95        33.04        13.78        90.28        30.15 
TCGA-DD-A4NR TCGA-DD-A73G TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACY TCGA-DD-AACZ 
        0.30       114.35        53.19         0.30        47.67         5.62 
TCGA-DD-AADR TCGA-DD-AAEI TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E 
       66.67        50.33         9.73         0.20         0.20        13.41 
TCGA-EP-A3JL TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 
        9.96        27.88        51.06         1.84        11.80         2.14 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75C TCGA-NI-A8LF TCGA-PD-A5DF TCGA-UB-A7ME 
        3.72        11.84         9.57        19.92        21.01        15.98 
TCGA-WQ-A9G7 
        0.99 

$`12Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       27.88        40.41        41.33        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       37.25        20.81        14.99         1.18         8.55        13.02 
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
        8.61        10.59         0.66        11.97        11.08         1.51 
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        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 
       12.72        18.48        44.81        13.45        36.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.19         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
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-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 
       70.06        17.59        20.12       102.74       107.11         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ 
       30.61        33.14        32.52        30.97        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        35.67        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41        69.11         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       46.82         5.59         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       14.33        15.58        18.21        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       21.17        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        23.64        25.78        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO 
       12.69        15.85        13.91        13.35        12.82        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       20.61        19.59         0.62        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       60.89        23.97        19.10         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.03         0.33        81.73         0.39        13.68        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        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       20.42        17.10         7.76        12.03         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
        8.55         9.70         9.17         0.89         8.75         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       16.83         2.14        13.38        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03        16.67        18.38        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       10.85        58.88        17.69         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.04        15.39        15.52        24.13         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       19.76        16.44         1.71         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34        12.99        24.85        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.20               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            120.82             113.00 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             12.95              19.59 
[1] "0.2 - 120.8 (12.9)" "0.0 - 113.0 (19.6)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q GAIN MUTATED        18        7         0         12          4
  12Q GAIN WILD-TYPE     150       77         3         47          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q GAIN MUTATED            2        0         0         0
  12Q GAIN WILD-TYPE          5        3         1         2
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  18                150
  STAGE II                  7                 77
  STAGE III                 0                  3
  STAGE IIIA               12                 47
  STAGE IIIB                4                  4
  STAGE IIIC                2                  5
  STAGE IV                  0                  3
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12Q GAIN MUTATED      19   7  16   2
  12Q GAIN WILD-TYPE   160  84  57  10
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1               19                160
  T2                   7                 84
  T3                  16                 57
  T4                   2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    32   1
  12Q GAIN WILD-TYPE 217   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     32    1
  12Q GAIN WILD-TYPE  217    2
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               32                217
  1                1                  2
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    36   0
  12Q GAIN WILD-TYPE 224   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     36    0
  12Q GAIN WILD-TYPE  224    4
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               36                224
  1                0                  4
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    18  26
  12Q GAIN WILD-TYPE  95 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     18   26
  12Q GAIN WILD-TYPE   95  218
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               18                 95
  MALE                 26                218
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12Q GAIN MUTATED                         0                       41
  12Q GAIN WILD-TYPE                       2                      307
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12Q GAIN MUTATED                                  3
  12Q GAIN WILD-TYPE                                4
D24V8, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       41                307
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    39   0   0   3
  12Q GAIN WILD-TYPE 276  15   1  16
D24V9, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               39                276
  R1                0                 15
  R2                0                  1
  RX                3                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0    19
  12Q GAIN WILD-TYPE                                1   137
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           2    22
  12Q GAIN WILD-TYPE                        15   151
D24V10, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          19                137
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          22                151
[1] 4 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     1  40
  12Q GAIN WILD-TYPE  10 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   40
  12Q GAIN WILD-TYPE   10  289
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               40                289
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    10  10
  13Q GAIN WILD-TYPE 215  99
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                20                314 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                 99 
$`13Q GAIN MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-BC-A3KF TCGA-BD-A3EP TCGA-CC-5263 TCGA-DD-A1EG 
       41.79        27.88         0.26        13.45         4.24        45.11 
TCGA-DD-A1EJ TCGA-DD-A3A7 TCGA-DD-AACB TCGA-DD-AACO TCGA-DD-AAE3 TCGA-DD-AAVW 
       33.04        13.78        76.41        61.68        18.61        76.18 
TCGA-ED-A66Y TCGA-EP-A3JL TCGA-FV-A23B TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-RC-A7S9 
        9.73         9.96        60.89        11.80         2.14        21.04 
TCGA-RG-A7D4 TCGA-UB-A7MC 
       24.13        16.44 

$`13Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        80.28        24.89 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        41.33        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        37.25        20.81        14.99         1.18         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
       13.02         8.61        10.78        10.59         0.66        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       11.08         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER 
       17.98        14.60        12.72        18.48        44.81        36.66 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
        0.66         0.07         2.86         3.19         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        11.47        12.95        49.15         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        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        90.28 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.87        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
       19.99         4.64        21.17        21.83        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ 
       19.59         0.62        11.93        22.85        14.40        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        81.73         0.39        13.68        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        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       11.24         8.55         9.70         9.17         0.89         8.75 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83         3.72         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       18.38        12.85        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF 
       19.92        17.69        21.01         3.09        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD 
       15.39        15.52         0.76        17.59        19.76         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.98         7.04        10.75        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       12.99        24.85        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.26               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             76.41             120.82 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            19.825             19.265 
[1] "0.3 - 76.4 (19.8)"  "0.0 - 120.8 (19.3)"
[1] "hr=" "1.6"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q GAIN MUTATED        10        3         0          5          1
  13Q GAIN WILD-TYPE     158       81         3         54          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q GAIN MUTATED            2        1         0         0
  13Q GAIN WILD-TYPE          5        2         1         2
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  10                158
  STAGE II                  3                 81
  STAGE III                 0                  3
  STAGE IIIA                5                 54
  STAGE IIIB                1                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  13Q GAIN MUTATED      11   4   6   1
  13Q GAIN WILD-TYPE   168  87  67  11
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               11                168
  T2                   4                 87
  T3                   6                 67
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    18   1
  13Q GAIN WILD-TYPE 231   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     18    1
  13Q GAIN WILD-TYPE  231    2
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               18                231
  1                1                  2
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    17   1
  13Q GAIN WILD-TYPE 243   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     17    1
  13Q GAIN WILD-TYPE  243    3
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               17                243
  1                1                  3
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    10  12
  13Q GAIN WILD-TYPE 103 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     10   12
  13Q GAIN WILD-TYPE  103  232
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               10                103
  MALE                 12                232
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  13Q GAIN MUTATED                         0                       22
  13Q GAIN WILD-TYPE                       2                      326
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  13Q GAIN MUTATED                                  0
  13Q GAIN WILD-TYPE                                7
D25V8, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       22                326
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of 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    19   0   0   2
  13Q GAIN WILD-TYPE 296  15   1  17
D25V9, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               19                296
  R1                0                 15
  R2                0                  1
  RX                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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     9
  13Q GAIN WILD-TYPE                                1   147
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           2    10
  13Q GAIN WILD-TYPE                        15   163
D25V10, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                147
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          10                163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1  19
  13Q GAIN WILD-TYPE  10 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   19
  13Q GAIN WILD-TYPE   10  310
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               19                310
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    14   9
  14Q GAIN WILD-TYPE 211 100
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                23                311 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                100 
$`14Q GAIN MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-BD-A2L6 
       41.79        27.88        56.91        20.81        13.02        44.81 
TCGA-BD-A3EP TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A4ND TCGA-DD-AACB 
       13.45         0.10        37.78         7.33        90.28        76.41 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ES-A2HS TCGA-FV-A3I0 
       18.61         4.64         9.73        14.04        22.85        27.88 
TCGA-G3-A3CG TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-UB-A7ME TCGA-YA-A8S7 
       22.13         2.14        11.84        15.98        13.55 

$`14Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        80.28        24.89 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
      120.82        40.41        41.33        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG 
       37.25        14.99         1.18         8.55         8.61        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.59         0.66        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       12.72        18.48        36.66         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        3.19         3.39         4.24         3.32         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.13        79.73        83.57        53.33       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        33.14        32.52        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        75.65        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       14.33        66.67        15.58        18.21        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 
       18.25        18.25        18.15        20.98        19.99        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.83        23.74        18.90        15.72        25.08        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       23.64        25.78        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        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        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       11.93        14.40        60.89        23.97        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38        12.03         0.03         0.33        81.73         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       13.68        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        5.98         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.17         0.89         8.75         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        13.38        24.36        12.72        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
        9.57        16.67        18.38        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        19.92        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
        0.76        17.59        19.76        16.44         1.71         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       10.75        10.32        11.34         0.99        12.99        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        40.80        79.30        11.21 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.10               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             90.28             120.82 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             18.61              19.30 
[1] "0.1 - 90.3 (18.6)"  "0.0 - 120.8 (19.3)"
[1] "hr=" "1.3"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q GAIN MUTATED        11        4         0          5          1
  14Q GAIN WILD-TYPE     157       80         3         54          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q GAIN MUTATED            0        1         0         0
  14Q GAIN WILD-TYPE          7        2         1         2
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  11                157
  STAGE II                  4                 80
  STAGE III                 0                  3
  STAGE IIIA                5                 54
  STAGE IIIB                1                  7
  STAGE IIIC                0                  7
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  14Q GAIN MUTATED      12   4   7   0
  14Q GAIN WILD-TYPE   167  87  66  12
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1               12                167
  T2                   4                 87
  T3                   7                 66
  T4                   0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    15   0
  14Q GAIN WILD-TYPE 234   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15    0
  14Q GAIN WILD-TYPE  234    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               15                234
  1                0                  3
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    13   1
  14Q GAIN WILD-TYPE 247   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     13    1
  14Q GAIN WILD-TYPE  247    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               13                247
  1                1                  3
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    10  13
  14Q GAIN WILD-TYPE 103 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10   13
  14Q GAIN WILD-TYPE  103  231
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               10                103
  MALE                 13                231
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  14Q GAIN MUTATED                         0                       21
  14Q GAIN WILD-TYPE                       2                      327
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  14Q GAIN MUTATED                                  2
  14Q GAIN WILD-TYPE                                5
D26V8, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       21                327
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    20   1   1   1
  14Q GAIN WILD-TYPE 295  14   0  18
D26V9, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               20                295
  R1                1                 14
  R2                1                  0
  RX                1                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     8
  14Q GAIN WILD-TYPE                                1   148
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           3    12
  14Q GAIN WILD-TYPE                        14   161
D26V10, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                148
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          12                161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  20
  14Q GAIN WILD-TYPE  10 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   20
  14Q GAIN WILD-TYPE   10  309
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               20                309
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    24   7
  15Q GAIN WILD-TYPE 201 102
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                31                303 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                102 
$`15Q GAIN MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-BC-A10Q 
       23.80        27.88        56.91         8.55        10.78        37.32 
TCGA-BC-A10Y TCGA-BC-A3KG TCGA-CC-A3M9 TCGA-DD-A4NI TCGA-DD-A4NV TCGA-DD-A73G 
       23.34        22.36         0.10        26.83        78.84       114.35 
TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAE8 
       76.41        13.64         5.62        18.21        18.61        21.83 
TCGA-DD-AAEA TCGA-DD-AAEK TCGA-ED-A66X TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A4ZQ 
       18.90        35.08        13.35         1.84        22.85         0.39 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A6UC TCGA-MI-A75G TCGA-MR-A8JO TCGA-RC-A7SK 
       51.06        58.49         7.76        18.38        10.85        15.52 
TCGA-WQ-AB4B 
       12.99 

$`15Q GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
      120.82        40.41        41.33        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-4R-AA8I 
       37.25        20.81        14.99         1.18        13.02         8.61 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.59         0.66        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       25.32         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
        0.26        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.45        36.66         0.66         0.07         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-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        11.47        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        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05        22.78         1.45        35.67        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       11.41        75.65        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       58.16        42.81        61.68        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.87        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       19.99         4.64        21.17        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        23.64        25.78        50.33        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        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         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20        14.04        13.15        13.41        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38        12.03         0.03         0.33        81.73 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       22.95        20.42        17.10        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14         3.02         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.91        20.75        17.06        16.83         3.72         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       11.84        13.38        24.36        12.72        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 
        9.57        16.67        12.85        20.71         0.62        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       19.92        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       16.44         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34         0.99        24.85        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.10               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            114.35             120.82 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              18.9               19.3 
[1] "0.1 - 114.3 (18.9)" "0.0 - 120.8 (19.3)"
[1] "hr=" "1.5"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  15Q GAIN MUTATED        13        9         0          6          2
  15Q GAIN WILD-TYPE     155       75         3         53          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q GAIN MUTATED            0        1         0         0
  15Q GAIN WILD-TYPE          7        2         1         2
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  13                155
  STAGE II                  9                 75
  STAGE III                 0                  3
  STAGE IIIA                6                 53
  STAGE IIIB                2                  6
  STAGE IIIC                0                  7
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  15Q GAIN MUTATED      13  11   7   2
  15Q GAIN WILD-TYPE   166  80  66  10
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1               13                166
  T2                  11                 80
  T3                   7                 66
  T4                   2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    24   0
  15Q GAIN WILD-TYPE 225   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     24    0
  15Q GAIN WILD-TYPE  225    3
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               24                225
  1                0                  3
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    25   0
  15Q GAIN WILD-TYPE 235   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     25    0
  15Q GAIN WILD-TYPE  235    4
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               25                235
  1                0                  4
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     9  24
  15Q GAIN WILD-TYPE 104 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9   24
  15Q GAIN WILD-TYPE  104  220
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                9                104
  MALE                 24                220
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  15Q GAIN MUTATED                         1                       32
  15Q GAIN WILD-TYPE                       1                      316
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  15Q GAIN MUTATED                                  0
  15Q GAIN WILD-TYPE                                7
D27V8, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       32                316
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of 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    31   1   0   1
  15Q GAIN WILD-TYPE 284  14   1  18
D27V9, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               31                284
  R1                1                 14
  R2                0                  1
  RX                1                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0    15
  15Q GAIN WILD-TYPE                                1   141
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           0    17
  15Q GAIN WILD-TYPE                        17   156
D27V10, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          15                141
  BLACK OR AFRICAN AMERICAN                       0                 17
  WHITE                                          17                156
[1] 4 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     2  30
  15Q GAIN WILD-TYPE   9 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2   30
  15Q GAIN WILD-TYPE    9  299
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               30                299
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    20   7
  16P GAIN WILD-TYPE 205 102
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                27                307 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                102 
$`16P GAIN MUTATED`
TCGA-2Y-A9GY TCGA-3K-AAZ8 TCGA-5R-AA1D TCGA-BC-A10R TCGA-BC-A112 TCGA-DD-A113 
       24.89        13.02        11.08        10.13         5.03        79.73 
TCGA-DD-A11A TCGA-DD-A1EL TCGA-DD-A3A5 TCGA-DD-AACI TCGA-DD-AACT TCGA-DD-AADN 
        2.60        13.64       102.74        53.19        51.35        29.52 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A7PZ TCGA-ED-A82E 
       18.61        19.99        66.25        13.41         0.20        13.41 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SM TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-MR-A8JO 
       13.68        51.06        17.10        11.80        11.84        10.85 
TCGA-NI-A8LF TCGA-UB-A7MB TCGA-UB-AA0U 
       19.92        19.76        10.75 

$`16P GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55         8.61        10.78        10.59         0.66        11.97 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T 
        1.51        48.99        27.91        37.32        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        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       12.72        18.48        44.81        13.45        36.66         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.19         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        11.47 
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        33.04        18.35 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       21.14        27.19        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        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        59.31        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49        20.91         0.39        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       14.33        66.67        15.58        18.21        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        18.25        18.15        20.98         4.64        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.83        23.74        18.90        15.72        25.08        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       23.64        25.78        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       62.47        65.39        49.48        53.69        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       13.91        13.35         9.73         0.20        12.82        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       20.61        19.59         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        60.89        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38        12.03         0.03         0.33        81.73         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-A5SI 
       22.13        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       22.95        20.42         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       11.24         8.55         9.70         9.17         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       20.75        17.06        16.83         3.72         2.14        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V 
       18.38        12.85        20.71         0.62        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       21.01         3.09        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13         0.76        17.59        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.98         7.04        10.32        11.34         0.99        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        13.55        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.20               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            102.74             120.82 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             13.68              19.53 
[1] "0.2 - 102.7 (13.7)" "0.0 - 120.8 (19.5)"
[1] "hr=" "1.2"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED        10        9         1          4          1
  16P GAIN WILD-TYPE     158       75         2         55          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P GAIN MUTATED            1        0         0         0
  16P GAIN WILD-TYPE          6        3         1         2
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  10                158
  STAGE II                  9                 75
  STAGE III                 1                  2
  STAGE IIIA                4                 55
  STAGE IIIB                1                  7
  STAGE IIIC                1                  6
  STAGE IV                  0                  3
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16P GAIN MUTATED      10   9   8   1
  16P GAIN WILD-TYPE   169  82  65  11
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1               10                169
  T2                   9                 82
  T3                   8                 65
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    18   0
  16P GAIN WILD-TYPE 231   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     18    0
  16P GAIN WILD-TYPE  231    3
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               18                231
  1                0                  3
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    19   0
  16P GAIN WILD-TYPE 241   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     19    0
  16P GAIN WILD-TYPE  241    4
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               19                241
  1                0                  4
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     9  19
  16P GAIN WILD-TYPE 104 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9   19
  16P GAIN WILD-TYPE  104  225
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                9                104
  MALE                 19                225
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16P GAIN MUTATED                         1                       26
  16P GAIN WILD-TYPE                       1                      322
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16P GAIN MUTATED                                  1
  16P GAIN WILD-TYPE                                6
D28V8, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       26                322
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    24   2   0   2
  16P GAIN WILD-TYPE 291  13   1  17
D28V9, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               24                291
  R1                2                 13
  R2                0                  1
  RX                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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    11
  16P GAIN WILD-TYPE                                1   145
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           3    14
  16P GAIN WILD-TYPE                        14   159
D28V10, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          11                145
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          14                159
[1] 4 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  26
  16P GAIN WILD-TYPE  11 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   26
  16P GAIN WILD-TYPE   11  303
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               26                303
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    10   3
  16Q GAIN WILD-TYPE 215 106
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                321 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                106 
$`16Q GAIN MUTATED`
TCGA-3K-AAZ8 TCGA-5R-AA1D TCGA-DD-A1EL TCGA-DD-AACT TCGA-DD-AADN TCGA-DD-AAE3 
       13.02        11.08        13.64        51.35        29.52        18.61 
TCGA-ED-A82E TCGA-G3-A25T TCGA-G3-A5SM TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-MR-A8JO 
       13.41        51.06        17.10        11.80        11.84        10.85 
TCGA-YA-A8S7 
       13.55 

$`16Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55         8.61        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       11.97         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       22.36        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.45        36.66         0.66         0.07         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        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        33.04        18.35        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
       61.68        13.64        14.20        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO 
       35.67        35.05        34.49        20.91         0.39        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV 
       15.06        14.33        66.67        15.58        18.21        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       19.30        18.25        18.25        18.15        20.98        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        21.17        21.83        23.74        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       25.08        16.37        23.64        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.59         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       60.89        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
       12.03         0.03         0.33        81.73         0.39        13.68 
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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       22.95        20.42         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       11.24         8.55         9.70         9.17         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       20.75        17.06        16.83         3.72         2.14        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF 
       18.38        12.85        20.71         0.62        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       15.39        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       16.44         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34         0.99        12.99        24.85        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             10.85               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             51.35             120.82 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             13.55              19.59 
[1] "10.8 - 51.4 (13.6)" "0.0 - 120.8 (19.6)"
[1] "hr=" "1.1"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED         5        2         0          5          1
  16Q GAIN WILD-TYPE     163       82         3         54          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q GAIN MUTATED            1        0         0         0
  16Q GAIN WILD-TYPE          6        3         1         2
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   5                163
  STAGE II                  2                 82
  STAGE III                 0                  3
  STAGE IIIA                5                 54
  STAGE IIIB                1                  7
  STAGE IIIC                1                  6
  STAGE IV                  0                  3
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16Q GAIN MUTATED       5   2   6   1
  16Q GAIN WILD-TYPE   174  89  67  11
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                5                174
  T2                   2                 89
  T3                   6                 67
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    11   0
  16Q GAIN WILD-TYPE 238   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     11    0
  16Q GAIN WILD-TYPE  238    3
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               11                238
  1                0                  3
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    10   0
  16Q GAIN WILD-TYPE 250   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10    0
  16Q GAIN WILD-TYPE  250    4
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               10                250
  1                0                  4
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     4  10
  16Q GAIN WILD-TYPE 109 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4   10
  16Q GAIN WILD-TYPE  109  234
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                4                109
  MALE                 10                234
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16Q GAIN MUTATED                         1                       12
  16Q GAIN WILD-TYPE                       1                      336
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16Q GAIN MUTATED                                  1
  16Q GAIN WILD-TYPE                                6
D29V8, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       12                336
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    12   0   0   2
  16Q GAIN WILD-TYPE 303  15   1  17
D29V9, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               12                303
  R1                0                 15
  R2                0                  1
  RX                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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     6
  16Q GAIN WILD-TYPE                                1   150
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           2     6
  16Q GAIN WILD-TYPE                        15   167
D29V10, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                150
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                           6                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  11
  16Q GAIN WILD-TYPE  10 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   11
  16Q GAIN WILD-TYPE   10  318
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               11                318
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    19   8
  17P GAIN WILD-TYPE 206 101
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                27                307 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                101 
$`17P GAIN MUTATED`
TCGA-3K-AAZ8 TCGA-BC-A10Q TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A3A7 
       13.02        37.32         0.66         0.10        37.78        13.78 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACI 
       73.81       108.76        22.78        11.41        76.41        53.19 
TCGA-DD-AACS TCGA-DD-AAD0 TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AAE3 TCGA-ED-A66X 
       59.31         4.50        44.22        40.47        18.61        13.35 
TCGA-ED-A66Y TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-AAV6 
        9.73        19.59        22.85        81.73        30.74         2.14 
TCGA-NI-A8LF TCGA-UB-A7MA TCGA-UB-AA0U 
       19.92        17.59        10.75 

$`17P GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55         8.61        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
       11.97        11.08         1.51        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       22.36        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45        36.66         0.07         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.07         0.10         0.13        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11         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        90.28        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93         9.30        23.05         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
      114.35        13.48         0.53        75.65        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       63.48        12.00        15.42         6.41        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
        5.62        18.54        21.63        42.58        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.54        40.83        13.97        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.87        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
       19.99         4.64        21.17        21.83        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62         9.96        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        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-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
       11.80         9.70         9.17         0.89         8.75         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83         3.72         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85        20.71         0.62        10.85        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       21.01         3.09        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13         0.76        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.98         7.04        10.32        11.34         0.99        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        13.55        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.10               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            108.76             120.82 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             19.92              19.10 
[1] "0.1 - 108.8 (19.9)" "0.0 - 120.8 (19.1)"
[1] "hr=" "1.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P GAIN MUTATED        12        6         0          8          3
  17P GAIN WILD-TYPE     156       78         3         51          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P GAIN MUTATED            0        0         0         0
  17P GAIN WILD-TYPE          7        3         1         2
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  12                156
  STAGE II                  6                 78
  STAGE III                 0                  3
  STAGE IIIA                8                 51
  STAGE IIIB                3                  5
  STAGE IIIC                0                  7
  STAGE IV                  0                  3
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17P GAIN MUTATED      12   7  11   0
  17P GAIN WILD-TYPE   167  84  62  12
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1               12                167
  T2                   7                 84
  T3                  11                 62
  T4                   0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    20   0
  17P GAIN WILD-TYPE 229   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     20    0
  17P GAIN WILD-TYPE  229    3
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               20                229
  1                0                  3
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    22   0
  17P GAIN WILD-TYPE 238   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     22    0
  17P GAIN WILD-TYPE  238    4
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               22                238
  1                0                  4
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     9  21
  17P GAIN WILD-TYPE 104 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      9   21
  17P GAIN WILD-TYPE  104  223
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                9                104
  MALE                 21                223
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17P GAIN MUTATED                         0                       29
  17P GAIN WILD-TYPE                       2                      319
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17P GAIN MUTATED                                  1
  17P GAIN WILD-TYPE                                6
D30V8, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       29                319
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    24   4   0   2
  17P GAIN WILD-TYPE 291  11   1  17
D30V9, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               24                291
  R1                4                 11
  R2                0                  1
  RX                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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    14
  17P GAIN WILD-TYPE                                1   142
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           3    12
  17P GAIN WILD-TYPE                        14   161
D30V10, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          14                142
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          12                161
[1] 4 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  29
  17P GAIN WILD-TYPE  11 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   29
  17P GAIN WILD-TYPE   11  300
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               29                300
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    58  25
  17Q GAIN WILD-TYPE 167  84
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                83                251 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                25                 84 
$`17Q GAIN MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H9 TCGA-3K-AAZ8 TCGA-5R-AAAM 
       24.89       120.82        56.91        14.99        13.02         1.51 
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 
       48.99        37.32         2.99        23.34         1.12         5.03 
TCGA-BC-A217 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       13.84        14.60         0.66         2.86         3.19         4.24 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EI 
        0.13        37.78         7.33         2.60        79.40         6.02 
TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NO TCGA-DD-A4NP 
        5.62        17.59        13.78        30.61        73.81       108.76 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE 
       22.78         1.45        11.41        75.65        76.41        63.48 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD5 
       53.19        69.11        59.31         5.59         4.50        44.22 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADO TCGA-DD-AADR 
       13.97        40.47        39.52        37.64        14.89        66.67 
TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAEA TCGA-DD-AAEE TCGA-DD-AAW1 TCGA-ED-A66X 
       18.21        18.61        18.90        16.37        65.39        13.35 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
        9.73         0.20         1.84        19.59         0.62        22.85 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CK 
        0.03        81.73        53.79        30.74        21.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-MI-A75G 
       22.95        12.03        11.24         8.75         2.14        18.38 
TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       20.71        19.92        17.69        17.59        19.76        16.44 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-ZP-A9CZ TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       10.75        11.34        23.21        24.43        12.99 

$`17Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       27.88        40.41        41.33        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG 
       37.25        20.81         1.18         8.55         8.61        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10R 
       10.59         0.66        11.97        11.08        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A216 
       46.78        27.52        27.52        25.32        69.57        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
        0.26        22.36        17.98        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
       13.45        36.66         0.07         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-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        90.71        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ 
       75.65        11.47        12.95        45.11        49.15        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       18.35        13.64        21.14        27.19        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81         7.66        70.06        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        33.14        32.52        90.28        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ 
       26.83        30.51        39.78        56.25        29.56        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACC TCGA-DD-AACD 
       35.67       114.35        13.48         0.53        55.40        12.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       12.00        15.42         6.41         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU 
       42.81        61.68        13.64        14.20        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 
       50.33        46.82        47.67         5.62        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADF 
       42.58        22.09        40.08        40.54        40.83         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       15.06        14.33        15.58        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        18.15        20.98        19.99         4.64        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH 
       21.83        23.74        15.72        25.08        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20        12.82        14.04        13.15        13.41        13.35 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        18.74        19.99        20.61         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        60.89        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        6.38        12.03         0.33         0.39        13.68        51.06 
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-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       19.53        25.25        20.42        17.10         7.76         5.98 
TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83         3.72         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 
       12.85         0.62        10.85        58.88        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WQ-A9G7 
        0.76         1.71        15.98         7.04        10.32         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
       12.99        24.85        13.55        35.77        25.71        23.57 
TCGA-ZP-A9D1 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
        0.69        45.57        40.80        79.30        11.21 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.03               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            120.82             114.35 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             17.69              19.99 
[1] "0.0 - 120.8 (17.7)" "0.1 - 114.3 (20.0)"
[1] "hr=" "1"  
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED        38       20         0         19          4
  17Q GAIN WILD-TYPE     130       64         3         40          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q GAIN MUTATED            1        1         0         1
  17Q GAIN WILD-TYPE          6        2         1         1
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  38                130
  STAGE II                 20                 64
  STAGE III                 0                  3
  STAGE IIIA               19                 40
  STAGE IIIB                4                  4
  STAGE IIIC                1                  6
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17Q GAIN MUTATED      40  23  24   5
  17Q GAIN WILD-TYPE   139  68  49   7
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1               40                139
  T2                  23                 68
  T3                  24                 49
  T4                   5                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    62   0
  17Q GAIN WILD-TYPE 187   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     62    0
  17Q GAIN WILD-TYPE  187    3
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               62                187
  1                0                  3
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    64   2
  17Q GAIN WILD-TYPE 196   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     64    2
  17Q GAIN WILD-TYPE  196    2
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               64                196
  1                2                  2
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    23  69
  17Q GAIN WILD-TYPE  90 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     23   69
  17Q GAIN WILD-TYPE   90  175
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               23                 90
  MALE                 69                175
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17Q GAIN MUTATED                         0                       91
  17Q GAIN WILD-TYPE                       2                      257
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17Q GAIN MUTATED                                  1
  17Q GAIN WILD-TYPE                                6
D31V8, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       91                257
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    77   7   1   7
  17Q GAIN WILD-TYPE 238   8   0  12
D31V9, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               77                238
  R1                7                  8
  R2                1                  0
  RX                7                 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 GAIN MUTATED                                  0    47
  17Q GAIN WILD-TYPE                                1   109
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           6    36
  17Q GAIN WILD-TYPE                        11   137
D31V10, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          47                109
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          36                137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     3  87
  17Q GAIN WILD-TYPE   8 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3   87
  17Q GAIN WILD-TYPE    8  242
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               87                242
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    20   9
  18P GAIN WILD-TYPE 205 100
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                29                305 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                100 
$`18P GAIN MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H7 TCGA-3K-AAZ8 TCGA-BW-A5NO 
       23.80        24.89        56.91        37.25        13.02         0.66 
TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN TCGA-DD-AACF 
        4.24         0.13        79.73         7.33        29.56        12.00 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADR TCGA-DD-AAE9 
       13.97        40.47         3.78        35.05        66.67        23.74 
TCGA-DD-AAVP TCGA-ED-A66X TCGA-EP-A3JL TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
       79.07        13.35         9.96        81.73        51.06        58.49 
TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-ZP-A9CZ TCGA-ZP-A9D1 
       15.39        24.13         0.99        23.21         0.69 

$`18P GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
      120.82        40.41        41.33        47.74        18.25        11.74 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG 
       20.81        14.99         1.18         8.55         8.61        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.59         0.66        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 
       12.72        18.48        44.81        13.45        36.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.19         3.39         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.10        37.78        83.57        53.33       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        90.28        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       26.83        30.51        39.78        56.25        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       63.48        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE 
       44.22        22.09        40.08        40.54        40.83        39.52 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       37.64        35.67        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV 
       14.89        15.06        14.33        15.58        18.21        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB 
       19.99         4.64        21.17        21.83        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       25.08        16.37        23.64        25.78        50.33        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       13.41        12.69        15.85        13.91         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62        11.93        22.85        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33         0.39        13.68        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        25.25        22.95        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       12.03         5.98         1.84        11.24         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
        9.70         9.17         0.89         8.75         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83         3.72         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85        20.71         0.62        10.85        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52         0.76        17.59        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
       15.98         7.04        10.75        10.32        11.34        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       24.85        13.55        35.77        25.71        23.57        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        40.80        79.30        11.21 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.13               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             81.73             120.82 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             23.74              19.10 
[1] "0.1 - 81.7 (23.7)"  "0.0 - 120.8 (19.1)"
[1] "hr=" "1.1"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P GAIN MUTATED        12        8         0          9          1
  18P GAIN WILD-TYPE     156       76         3         50          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P GAIN MUTATED            0        2         0         0
  18P GAIN WILD-TYPE          7        1         1         2
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  12                156
  STAGE II                  8                 76
  STAGE III                 0                  3
  STAGE IIIA                9                 50
  STAGE IIIB                1                  7
  STAGE IIIC                0                  7
  STAGE IV                  2                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18P GAIN MUTATED      14   9  12   0
  18P GAIN WILD-TYPE   165  82  61  12
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1               14                165
  T2                   9                 82
  T3                  12                 61
  T4                   0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    26   0
  18P GAIN WILD-TYPE 223   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     26    0
  18P GAIN WILD-TYPE  223    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               26                223
  1                0                  3
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    25   1
  18P GAIN WILD-TYPE 235   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     25    1
  18P GAIN WILD-TYPE  235    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               25                235
  1                1                  3
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    10  25
  18P GAIN WILD-TYPE 103 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     10   25
  18P GAIN WILD-TYPE  103  219
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               10                103
  MALE                 25                219
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18P GAIN MUTATED                         0                       35
  18P GAIN WILD-TYPE                       2                      313
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18P GAIN MUTATED                                  0
  18P GAIN WILD-TYPE                                7
D32V8, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       35                313
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of 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    29   1   1   3
  18P GAIN WILD-TYPE 286  14   0  16
D32V9, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               29                286
  R1                1                 14
  R2                1                  0
  RX                3                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0    21
  18P GAIN WILD-TYPE                                1   135
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           3    11
  18P GAIN WILD-TYPE                        14   162
D32V10, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          21                135
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          11                162
[1] 4 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     1  34
  18P GAIN WILD-TYPE  10 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   34
  18P GAIN WILD-TYPE   10  295
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               34                295
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    14   8
  18Q GAIN WILD-TYPE 211 101
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                22                312 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                101 
$`18Q GAIN MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-3K-AAZ8 TCGA-BW-A5NO TCGA-CC-5263 
       23.80        24.89        56.91        13.02         0.66         4.24 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN TCGA-DD-AACF TCGA-DD-AADC 
        0.13        79.73         7.33        29.56        12.00        13.97 
TCGA-DD-AADD TCGA-DD-AADJ TCGA-DD-AADR TCGA-DD-AAE3 TCGA-EP-A3JL TCGA-FV-A4ZP 
       40.47        35.05        66.67        18.61         9.96        81.73 
TCGA-G3-A25T TCGA-G3-A25X TCGA-RC-A7SH TCGA-ZP-A9D1 
       51.06        58.49        15.39         0.69 

$`18Q GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
      120.82        40.41        41.33        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I 
       37.25        20.81        14.99         1.18         8.55         8.61 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        11.97        11.08         1.51 
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        17.98 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER 
       14.60        12.72        18.48        44.81        13.45        36.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         2.86         3.19         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10        37.78        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        11.47        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        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO 
       30.15        26.83        30.51        39.78        56.25        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        63.48        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL 
       39.52         3.78        37.64        35.67        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
        0.39        29.52        14.89        15.06        14.33        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       18.21        18.87        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       20.98        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       18.90        15.72        25.08        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        49.48        53.69        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         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
        8.12         6.38        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        11.24         8.55        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        11.84        13.38        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        0.62        10.85        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 
        3.09        21.04        19.33        19.04        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
        0.76        17.59        19.76        16.44         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        7.04        10.75        10.32        11.34         0.99        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        13.55        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        40.80        79.30        11.21 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.13               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             81.73             120.82 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            21.205             19.265 
[1] "0.1 - 81.7 (21.2)"  "0.0 - 120.8 (19.3)"
[1] "hr=" "1.1"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18Q GAIN MUTATED         9        6         0          8          1
  18Q GAIN WILD-TYPE     159       78         3         51          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q GAIN MUTATED            0        2         0         0
  18Q GAIN WILD-TYPE          7        1         1         2
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   9                159
  STAGE II                  6                 78
  STAGE III                 0                  3
  STAGE IIIA                8                 51
  STAGE IIIB                1                  7
  STAGE IIIC                0                  7
  STAGE IV                  2                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18Q GAIN MUTATED      10   7  10   0
  18Q GAIN WILD-TYPE   169  84  63  12
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1               10                169
  T2                   7                 84
  T3                  10                 63
  T4                   0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    20   0
  18Q GAIN WILD-TYPE 229   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     20    0
  18Q GAIN WILD-TYPE  229    3
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               20                229
  1                0                  3
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    19   1
  18Q GAIN WILD-TYPE 241   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     19    1
  18Q GAIN WILD-TYPE  241    3
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               19                241
  1                1                  3
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     7  20
  18Q GAIN WILD-TYPE 106 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7   20
  18Q GAIN WILD-TYPE  106  224
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                7                106
  MALE                 20                224
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18Q GAIN MUTATED                         0                       27
  18Q GAIN WILD-TYPE                       2                      321
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18Q GAIN MUTATED                                  0
  18Q GAIN WILD-TYPE                                7
D33V8, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       27                321
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of 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    21   1   1   3
  18Q GAIN WILD-TYPE 294  14   0  16
D33V9, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               21                294
  R1                1                 14
  R2                1                  0
  RX                3                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0    16
  18Q GAIN WILD-TYPE                                1   140
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           2     9
  18Q GAIN WILD-TYPE                        15   164
D33V10, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          16                140
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                           9                164
[1] 4 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     1  26
  18Q GAIN WILD-TYPE  10 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   26
  18Q GAIN WILD-TYPE   10  303
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               26                303
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    32  19
  19P GAIN WILD-TYPE 193  90
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                51                283 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                19                 90 
$`19P GAIN MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-3K-AAZ8 TCGA-BC-A10Q TCGA-BD-A3EP TCGA-BW-A5NO 
       63.75        41.79        13.02        37.32        13.45         0.66 
TCGA-CC-5261 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC 
        3.19        79.73       113.00         7.33        90.71        19.79 
TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND 
       12.95        21.14        55.69        13.78        30.61        90.28 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACT 
       29.56        73.81        12.26        78.84       114.35        51.35 
TCGA-DD-AACW TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAEK 
       46.82        40.83         3.78        18.25        18.61        35.08 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A2KC 
        9.73         0.20        14.04        13.41        19.59         0.62 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25X 
       22.85        60.89        23.97        27.88        51.06        58.49 
TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-KR-A7K2 TCGA-MI-A75G TCGA-RC-A7S9 
       17.10         5.98         8.55        11.84        18.38        21.04 
TCGA-RC-A7SH TCGA-YA-A8S7 TCGA-ZP-A9D1 
       15.39        13.55         0.69 

$`19P GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       23.80        53.39        83.24        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        41.33        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        37.25        20.81        14.99         1.18         8.55 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.61        10.78        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
        1.51        48.99        27.91        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        17.98 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5258 
       14.60        12.72        18.48        44.81        36.66         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-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-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       11.47        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        27.19         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 
       70.06        17.59        20.12       102.74       107.11         0.36 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       39.78        56.25       108.76         0.30        80.75        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
        9.30        23.05        22.78         1.45        35.67        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       63.48        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY 
       14.20        59.31        51.52        50.33         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.08        40.54        13.97        40.47        39.52 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        18.87        19.30        18.25        18.15        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
       19.99         4.64        21.17        21.83        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        12.82        13.15        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61         9.96        11.93        14.40 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10         8.12         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       81.73         0.39        13.68        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-A7M6 
       19.23        25.25        22.95        20.42         7.76        12.03 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24        11.80         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14         3.02         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.91        20.75        17.06        16.83         3.72         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        12.85        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF 
       19.92        17.69        21.01         3.09        19.33        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.52        24.13         0.76        17.59        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
        1.71        15.98         7.04        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99        12.99        24.85        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57        24.43        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.20               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            114.35             120.82 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             19.79              19.10 
[1] "0.2 - 114.3 (19.8)" "0.0 - 120.8 (19.1)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P GAIN MUTATED        23       13         0          9          2
  19P GAIN WILD-TYPE     145       71         3         50          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P GAIN MUTATED            0        2         1         1
  19P GAIN WILD-TYPE          7        1         0         1
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  23                145
  STAGE II                 13                 71
  STAGE III                 0                  3
  STAGE IIIA                9                 50
  STAGE IIIB                2                  6
  STAGE IIIC                0                  7
  STAGE IV                  2                  1
  STAGE IVA                 1                  0
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19P GAIN MUTATED      25  15  12   1
  19P GAIN WILD-TYPE   154  76  61  11
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1               25                154
  T2                  15                 76
  T3                  12                 61
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    38   1
  19P GAIN WILD-TYPE 211   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     38    1
  19P GAIN WILD-TYPE  211    2
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               38                211
  1                1                  2
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    38   3
  19P GAIN WILD-TYPE 222   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     38    3
  19P GAIN WILD-TYPE  222    1
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               38                222
  1                3                  1
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    24  29
  19P GAIN WILD-TYPE  89 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     24   29
  19P GAIN WILD-TYPE   89  215
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               24                 89
  MALE                 29                215
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19P GAIN MUTATED                         0                       51
  19P GAIN WILD-TYPE                       2                      297
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19P GAIN MUTATED                                  2
  19P GAIN WILD-TYPE                                5
D34V8, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       51                297
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    47   1   1   4
  19P GAIN WILD-TYPE 268  14   0  15
D34V9, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               47                268
  R1                1                 14
  R2                1                  0
  RX                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0    18
  19P GAIN WILD-TYPE                                1   138
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           4    30
  19P GAIN WILD-TYPE                        13   143
D34V10, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          18                138
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          30                143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  48
  19P GAIN WILD-TYPE   8 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   48
  19P GAIN WILD-TYPE    8  281
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               48                281
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    43  23
  19Q GAIN WILD-TYPE 182  86
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                66                268 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                 86 
$`19Q GAIN MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9H3 TCGA-3K-AAZ8 TCGA-BC-A10Q TCGA-BC-A10R 
       63.75        41.79        41.33        13.02        37.32        10.13 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A118 
       13.45         0.66         3.19         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        90.28        29.56        73.81        12.26 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT 
       78.84       114.35        15.42        61.68        13.64        51.35 
TCGA-DD-AACW TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADM 
       46.82        40.83        13.97        40.47         3.78         0.39 
TCGA-DD-AAE0 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEK TCGA-ED-A66Y TCGA-ED-A7PZ 
       18.25        21.17        18.90        35.08         9.73         0.20 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B 
       14.04        13.41        19.59         0.62        22.85        60.89 
TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM 
       23.97        27.88         0.39        51.06        58.49        17.10 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-KR-A7K2 TCGA-MI-A75G TCGA-NI-A8LF 
       12.03         5.98         8.55        11.84        18.38        19.92 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7ME TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 
       21.04        15.39        15.98        12.99        13.55         0.69 

$`19Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       23.80        53.39        83.24        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
      120.82        40.41        56.91        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I 
       37.25        20.81        14.99         1.18         8.55         8.61 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        11.97        11.08         1.51 
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        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 
       18.48        44.81        36.66         0.07         2.86         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 
        4.24         3.32         0.07         0.10         0.13        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57        53.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       79.40        66.31        75.65        11.47        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z 
       33.04        18.35        13.64        27.19         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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78         0.36        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       30.15        26.83        30.51        39.78        56.25       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        35.67        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
       76.41        55.40        12.53        63.48        12.00         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY 
       14.20        59.31        51.52        50.33         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI 
       22.09        40.08        40.54        39.52        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49        20.91        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       14.33        66.67        15.58        18.21        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       21.83        23.74        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        49.48        53.69        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 
       13.91        13.35         0.20        12.82        13.15        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        1.84         0.20        18.74        19.99        20.61         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       11.93        14.40        19.10         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        81.73        13.68        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       19.53        19.23        25.25        22.95        20.42         7.76 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24        11.80         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14         3.02         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.91        20.75        17.06        16.83         3.72         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        12.85        20.71         0.62        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK 
       17.69        21.01         3.09        19.33        19.04        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       24.13         0.76        17.59        19.76        16.44         1.71 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 
        7.04        10.75        10.32        11.34         0.99        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.10               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            114.35             120.82 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            19.245             19.265 
[1] "0.1 - 114.3 (19.2)" "0.0 - 120.8 (19.3)"
[1] "hr=" "1"  
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED        33       17         0         10          1
  19Q GAIN WILD-TYPE     135       67         3         49          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q GAIN MUTATED            0        2         1         1
  19Q GAIN WILD-TYPE          7        1         0         1
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  33                135
  STAGE II                 17                 67
  STAGE III                 0                  3
  STAGE IIIA               10                 49
  STAGE IIIB                1                  7
  STAGE IIIC                0                  7
  STAGE IV                  2                  1
  STAGE IVA                 1                  0
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19Q GAIN MUTATED      35  19  13   1
  19Q GAIN WILD-TYPE   144  72  60  11
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1               35                144
  T2                  19                 72
  T3                  13                 60
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    46   1
  19Q GAIN WILD-TYPE 203   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     46    1
  19Q GAIN WILD-TYPE  203    2
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               46                203
  1                1                  2
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    48   3
  19Q GAIN WILD-TYPE 212   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     48    3
  19Q GAIN WILD-TYPE  212    1
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               48                212
  1                3                  1
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    26  42
  19Q GAIN WILD-TYPE  87 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     26   42
  19Q GAIN WILD-TYPE   87  202
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               26                 87
  MALE                 42                202
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19Q GAIN MUTATED                         0                       66
  19Q GAIN WILD-TYPE                       2                      282
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19Q GAIN MUTATED                                  2
  19Q GAIN WILD-TYPE                                5
D35V8, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       66                282
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    62   1   1   4
  19Q GAIN WILD-TYPE 253  14   0  15
D35V9, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               62                253
  R1                1                 14
  R2                1                  0
  RX                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0    27
  19Q GAIN WILD-TYPE                                1   129
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           4    37
  19Q GAIN WILD-TYPE                        13   136
D35V10, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          27                129
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          37                136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     4  63
  19Q GAIN WILD-TYPE   7 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      4   63
  19Q GAIN WILD-TYPE    7  266
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               63                266
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    56  40
  20P GAIN WILD-TYPE 169  69
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                96                238 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                40                 69 
$`20P GAIN MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       23.80        80.28        24.89        27.88        20.81        14.99 
TCGA-2Y-A9HA TCGA-5C-A9VH TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R 
        1.18        10.59         1.51        48.99        37.32        10.13 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       13.84         0.26        14.60        44.81        13.45         0.66 
TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        3.19         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        33.04        21.14 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NR TCGA-DD-A4NV 
       13.78        30.61        90.28        29.56         0.30        78.84 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACH TCGA-DD-AACI 
      114.35         0.53        76.41        55.40         6.41        53.19 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD6 
       61.68        13.64        51.35        50.33         5.62        22.09 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS 
       40.47         3.78        37.64        29.52        14.89        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEH 
       18.21        19.30        18.25        18.61        23.74        25.78 
TCGA-DD-AAEK TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O6 
       35.08        13.35         9.73        14.04        13.41         1.84 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 TCGA-FV-A4ZQ 
       19.59         9.96        22.85        60.89         6.38         0.39 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       13.68        58.49        14.86        17.10         7.76        12.03 
TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-KR-A7K2 
        1.84        11.80         0.89         2.14         2.99        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A8LF TCGA-RG-A7D4 TCGA-UB-A7MA 
       13.38        12.72        18.38        19.92        24.13        17.59 
TCGA-UB-A7MB TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZS-A9CD 
       19.76        10.75         0.99        12.99        13.55        45.57 

$`20P GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       53.39        63.75        83.24        41.79       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       56.91        41.33        47.74        18.25        11.74        37.25 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55        13.02         8.61        10.78         0.66        11.97 
TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       11.08        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-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 
       22.36        17.98        12.72        18.48        36.66         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC 
        2.86         3.39         4.24         3.32         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11C TCGA-DD-A11D 
       79.73        37.78        83.57        53.33        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        11.47 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        18.35        13.64        27.19        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11         0.36        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO 
       30.15        26.83        30.51        39.78        56.25        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
      108.76        12.26        80.75        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA 
       22.78         1.45        35.67        13.48        11.41        75.65 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACJ TCGA-DD-AACK 
       12.53        63.48        12.00        15.42        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        3.52        58.16        42.81        14.20        59.31        51.52 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       42.58        44.22        40.08        40.54        40.83        13.97 
TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       39.52        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE1 
       15.06        14.33        66.67        18.87        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
       20.98        19.99         4.64        21.17        21.83        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAVP 
       15.72        25.08        16.37        23.64        50.33        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       13.41        12.69        15.85        13.91         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
        0.20        13.15        13.35         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR 
       20.61         0.62        11.93        14.40        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         8.12        12.03         0.03         0.33        81.73 
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        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       20.42         5.98        11.24         8.55         9.70         9.17 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF 
        8.75         3.02         1.02         2.20        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83         3.72         2.14        24.36        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       10.85        58.88        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MC 
       19.33        19.04        15.39        15.52         0.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 
        1.71        15.98         7.04        10.32        11.34        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        40.80        79.30        11.21 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.10               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            114.35             120.82 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            14.940             20.515 
[1] "0.1 - 114.3 (14.9)" "0.0 - 120.8 (20.5)"
[1] "hr=" "1.7"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED        42       26         1         22          4
  20P GAIN WILD-TYPE     126       58         2         37          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P GAIN MUTATED            2        3         0         1
  20P GAIN WILD-TYPE          5        0         1         1
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  42                126
  STAGE II                 26                 58
  STAGE III                 1                  2
  STAGE IIIA               22                 37
  STAGE IIIB                4                  4
  STAGE IIIC                2                  5
  STAGE IV                  3                  0
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20P GAIN MUTATED      44  29  29   3
  20P GAIN WILD-TYPE   135  62  44   9
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               44                135
  T2                  29                 62
  T3                  29                 44
  T4                   3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    73   1
  20P GAIN WILD-TYPE 176   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     73    1
  20P GAIN WILD-TYPE  176    2
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               73                176
  1                1                  2
[1] 2 2
[1] FALSE
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    79   3
  20P GAIN WILD-TYPE 181   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     79    3
  20P GAIN WILD-TYPE  181    1
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               79                181
  1                3                  1
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    39  66
  20P GAIN WILD-TYPE  74 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     39   66
  20P GAIN WILD-TYPE   74  178
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               39                 74
  MALE                 66                178
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20P GAIN MUTATED                         0                      103
  20P GAIN WILD-TYPE                       2                      245
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20P GAIN MUTATED                                  2
  20P GAIN WILD-TYPE                                5
D36V8, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                      103                245
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED    92   6   1   5
  20P GAIN WILD-TYPE 223   9   0  14
D36V9, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               92                223
  R1                6                  9
  R2                1                  0
  RX                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0    44
  20P GAIN WILD-TYPE                                1   112
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           4    55
  20P GAIN WILD-TYPE                        13   118
D36V10, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          44                112
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          55                118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     3  95
  20P GAIN WILD-TYPE   8 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3   95
  20P GAIN WILD-TYPE    8  234
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               95                234
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    62  38
  20Q GAIN WILD-TYPE 163  71
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               100                234 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                38                 71 
$`20Q GAIN MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       23.80        80.28        24.89        27.88        20.81        14.99 
TCGA-2Y-A9HA TCGA-5C-A9VH TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R 
        1.18        10.59         1.51        48.99        37.32        10.13 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       13.84         0.26        14.60        44.81        13.45         0.66 
TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A118 TCGA-DD-A119 
        3.19         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-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN 
       33.04        21.14        13.78        30.61        90.28        29.56 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC 
        0.30        78.84       114.35         0.53        76.41        55.40 
TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV 
       53.19        61.68        13.64        59.31        51.35        50.33 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG 
        5.62         4.50        22.09        40.47         3.78        37.64 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 
       29.52        14.89        15.58        18.21        19.30        18.25 
TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEH TCGA-DD-AAEK TCGA-ED-A66X 
       18.61        23.74        18.90        25.78        35.08        13.35 
TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A3JL 
        9.73        14.04        13.41         1.84        19.59         9.96 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25X 
       22.85        60.89         6.38         0.39        13.68        58.49 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 
       17.10         7.76        12.03         1.84        11.80         2.14 
TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A8LF 
        2.99        11.84        13.38        12.72        18.38        19.92 
TCGA-PD-A5DF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U 
       21.01        24.13        17.59        19.76        15.98        10.75 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZS-A9CD 
        0.99        12.99        13.55        45.57 

$`20Q GAIN WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       53.39        63.75        83.24        41.79       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       56.91        41.33        47.74        18.25        11.74        37.25 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55        13.02         8.61        10.78         0.66        11.97 
TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       11.08        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-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 
       22.36        17.98        12.72        18.48        36.66         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A113 
        2.86         3.39         4.24         3.32         0.07        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       37.78        83.57        53.33        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK 
       66.31        19.79        75.65        11.47         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        27.19        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
        0.36        33.14        32.52        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        39.78        56.25        73.81       108.76        12.26 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE 
       35.67        13.48        11.41        75.65        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       58.16        42.81        14.20        51.52        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
       47.67        18.54        21.63        42.58        44.22        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADJ 
       40.54        40.83        13.97        39.52        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       34.49        20.91         0.39        15.06        14.33        66.67 
TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.87        18.25        18.15        20.98        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       21.17        21.83        15.72        25.08        16.37        23.64 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20        12.82         0.20        13.15        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61         0.62        11.93        14.40 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10        27.88         8.12        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33        81.73        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M7 TCGA-G3-AAUZ 
       19.23        25.25        22.95        20.42         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
        8.55         9.70         9.17         0.89         8.75         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20        37.91        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        3.72         2.14        24.36        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        12.85        20.71         0.62        10.85        58.88 
TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       17.69         3.09        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V 
       15.52         0.76        16.44         1.71         7.04        10.32 
TCGA-WJ-A86L TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       11.34        24.85        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
        0.69        24.43        12.99        40.80        79.30        11.21 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.10               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            114.35             120.82 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             16.54              20.27 
[1] "0.1 - 114.3 (16.5)" "0.0 - 120.8 (20.3)"
[1] "hr=" "1.5"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED        45       25         1         24          5
  20Q GAIN WILD-TYPE     123       59         2         35          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q GAIN MUTATED            2        2         0         1
  20Q GAIN WILD-TYPE          5        1         1         1
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  45                123
  STAGE II                 25                 59
  STAGE III                 1                  2
  STAGE IIIA               24                 35
  STAGE IIIB                5                  3
  STAGE IIIC                2                  5
  STAGE IV                  2                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20Q GAIN MUTATED      47  27  31   4
  20Q GAIN WILD-TYPE   132  64  42   8
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               47                132
  T2                  27                 64
  T3                  31                 42
  T4                   4                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    76   1
  20Q GAIN WILD-TYPE 173   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     76    1
  20Q GAIN WILD-TYPE  173    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               76                173
  1                1                  2
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    83   2
  20Q GAIN WILD-TYPE 177   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     83    2
  20Q GAIN WILD-TYPE  177    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               83                177
  1                2                  2
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    38  71
  20Q GAIN WILD-TYPE  75 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     38   71
  20Q GAIN WILD-TYPE   75  173
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               38                 75
  MALE                 71                173
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20Q GAIN MUTATED                         0                      107
  20Q GAIN WILD-TYPE                       2                      241
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20Q GAIN MUTATED                                  2
  20Q GAIN WILD-TYPE                                5
D37V8, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                      107                241
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED    95   6   1   5
  20Q GAIN WILD-TYPE 220   9   0  14
D37V9, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               95                220
  R1                6                  9
  R2                1                  0
  RX                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0    48
  20Q GAIN WILD-TYPE                                1   108
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           4    55
  20Q GAIN WILD-TYPE                        13   118
D37V10, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          48                108
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          55                118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     2 100
  20Q GAIN WILD-TYPE   9 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2  100
  20Q GAIN WILD-TYPE    9  229
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO              100                229
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    15   7
  21Q GAIN WILD-TYPE 210 102
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                22                312 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                102 
$`21Q GAIN MUTATED`
TCGA-2Y-A9GZ TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A217 TCGA-BW-A5NO 
       27.88        20.81        13.02        10.78        13.84         0.66 
TCGA-CC-5261 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A3A5 TCGA-DD-A4NV TCGA-DD-AAEK 
        3.19         4.24        79.73       102.74        78.84        35.08 
TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A3CG 
       13.41        19.59        22.85        27.88        51.06        22.13 
TCGA-G3-AAUZ TCGA-MI-A75G TCGA-RC-A7SH TCGA-UB-AA0U 
       11.24        18.38        15.39        10.75 

$`21Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       24.89       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       18.25        11.74        37.25        14.99         1.18         8.55 
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
        8.61        10.59         0.66        11.97        11.08         1.51 
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        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 
       12.72        18.48        44.81        13.45        36.66         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        2.86         3.39         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        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        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        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        90.28        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       63.48        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV 
       15.06        14.33        66.67        15.58        18.21        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
       19.99         4.64        21.17        21.83        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62         9.96        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10         8.12         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       81.73         0.39        13.68        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        25.25        22.95        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       12.03         5.98         1.84         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.17         0.89         8.75         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.91        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        3.72         2.14        11.84        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        0.62        10.85        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 
        3.09        21.04        19.33        19.04        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
        0.76        17.59        19.76        16.44         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
        7.04        10.32        11.34         0.99        12.99        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       13.55        35.77        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        40.80        79.30        11.21 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.66               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            102.74             120.82 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            18.985             19.265 
[1] "0.7 - 102.7 (19.0)" "0.0 - 120.8 (19.3)"
[1] "hr=" "1"  
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  21Q GAIN MUTATED         5       12         1          7          1
  21Q GAIN WILD-TYPE     163       72         2         52          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q GAIN MUTATED            0        0         0         0
  21Q GAIN WILD-TYPE          7        3         1         2
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   5                163
  STAGE II                 12                 72
  STAGE III                 1                  2
  STAGE IIIA                7                 52
  STAGE IIIB                1                  7
  STAGE IIIC                0                  7
  STAGE IV                  0                  3
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  21Q GAIN MUTATED       6  11   9   0
  21Q GAIN WILD-TYPE   173  80  64  12
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                6                173
  T2                  11                 80
  T3                   9                 64
  T4                   0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    16   0
  21Q GAIN WILD-TYPE 233   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     16    0
  21Q GAIN WILD-TYPE  233    3
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               16                233
  1                0                  3
[1] 2 2
[1] FALSE
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    18   0
  21Q GAIN WILD-TYPE 242   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     18    0
  21Q GAIN WILD-TYPE  242    4
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               18                242
  1                0                  4
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     9  17
  21Q GAIN WILD-TYPE 104 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9   17
  21Q GAIN WILD-TYPE  104  227
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                9                104
  MALE                 17                227
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  21Q GAIN MUTATED                         0                       25
  21Q GAIN WILD-TYPE                       2                      323
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  21Q GAIN MUTATED                                  1
  21Q GAIN WILD-TYPE                                6
D38V8, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       25                323
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    19   2   0   5
  21Q GAIN WILD-TYPE 296  13   1  14
D38V9, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               19                296
  R1                2                 13
  R2                0                  1
  RX                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     8
  21Q GAIN WILD-TYPE                                1   148
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           2    15
  21Q GAIN WILD-TYPE                        15   158
D38V10, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                148
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          15                158
[1] 4 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     1  24
  21Q GAIN WILD-TYPE  10 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   24
  21Q GAIN WILD-TYPE   10  305
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               24                305
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    28  13
  22Q GAIN WILD-TYPE 197  96
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                41                293 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                13                 96 
$`22Q GAIN MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9HA TCGA-3K-AAZ8 
       63.75        24.89        27.88        56.91         1.18        13.02 
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 
       10.13         5.03        14.60         0.66         0.07         3.19 
TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1EJ TCGA-DD-A4ND TCGA-DD-A73G 
        0.10       113.00        51.29        33.04        90.28       114.35 
TCGA-DD-AACB TCGA-DD-AACJ TCGA-DD-AAE0 TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVY 
       76.41        69.11        18.25        25.08        35.08        64.77 
TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A2QR 
       13.35         0.20        13.41         1.84        22.85        19.10 
TCGA-FV-A3I0 TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-UB-A7MA 
       27.88        58.49        22.13        12.03        11.80        17.59 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CG 
       15.98        10.75         0.99        13.55        11.21 

$`22Q GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 
       23.80        53.39        83.24        41.79        80.28       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       40.41        41.33        47.74        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
       20.81        14.99         8.55         8.61        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
        0.66        11.97        11.08         1.51        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        17.98        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
       36.66         2.86         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-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        21.76        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        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       49.15         6.02        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        33.14        32.52        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05        22.78         1.45        35.67        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       11.41        75.65        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42         6.41        53.19         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 
       15.58        18.21        18.87        19.30        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       20.98        18.61        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       23.74        18.90        15.72        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       76.18        56.48        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       53.69        13.41        12.69        15.85        13.91         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20        12.82        14.04        13.15        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.93        14.40        60.89        23.97         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
       12.03         0.03         0.33        81.73         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       20.42        17.10         7.76         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
        8.55         9.70         9.17         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83         3.72         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       18.38        12.85        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       19.92        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB 
       19.04        15.39        15.52        24.13         0.76        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
       16.44         1.71         7.04        10.32        11.34        12.99 
TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       24.85        35.77        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       24.43        12.99        45.57        40.80        79.30 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            114.35             120.82 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             17.59              19.53 
[1] "0.1 - 114.3 (17.6)" "0.0 - 120.8 (19.5)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  22Q GAIN MUTATED        12       17         0         12          2
  22Q GAIN WILD-TYPE     156       67         3         47          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q GAIN MUTATED            2        0         0         0
  22Q GAIN WILD-TYPE          5        3         1         2
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  12                156
  STAGE II                 17                 67
  STAGE III                 0                  3
  STAGE IIIA               12                 47
  STAGE IIIB                2                  6
  STAGE IIIC                2                  5
  STAGE IV                  0                  3
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  22Q GAIN MUTATED      13  17  16   2
  22Q GAIN WILD-TYPE   166  74  57  10
D39V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1               13                166
  T2                  17                 74
  T3                  16                 57
  T4                   2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    30   1
  22Q GAIN WILD-TYPE 219   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     30    1
  22Q GAIN WILD-TYPE  219    2
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               30                219
  1                1                  2
[1] 2 2
[1] FALSE
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    33   0
  22Q GAIN WILD-TYPE 227   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     33    0
  22Q GAIN WILD-TYPE  227    4
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               33                227
  1                0                  4
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    19  29
  22Q GAIN WILD-TYPE  94 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     19   29
  22Q GAIN WILD-TYPE   94  215
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               19                 94
  MALE                 29                215
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  22Q GAIN MUTATED                         0                       46
  22Q GAIN WILD-TYPE                       2                      302
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  22Q GAIN MUTATED                                  2
  22Q GAIN WILD-TYPE                                5
D39V8, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       46                302
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    40   3   0   5
  22Q GAIN WILD-TYPE 275  12   1  14
D39V9, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               40                275
  R1                3                 12
  R2                0                  1
  RX                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0    23
  22Q GAIN WILD-TYPE                                1   133
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           2    23
  22Q GAIN WILD-TYPE                        15   150
D39V10, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          23                133
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          23                150
[1] 4 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     1  47
  22Q GAIN WILD-TYPE  10 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   47
  22Q GAIN WILD-TYPE   10  282
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               47                282
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    23  13
  XP GAIN WILD-TYPE 202  96
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               36               298 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               13                96 
$`XP GAIN MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9H1 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10Z TCGA-BC-A3KF 
       41.79        40.41        10.13        27.52         1.12         0.26 
TCGA-CC-5260 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NK TCGA-DD-A4NV TCGA-DD-A73D 
        2.86        17.59        13.78        39.78        78.84        22.78 
TCGA-DD-A73G TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACT TCGA-DD-AAD2 TCGA-DD-AADU 
      114.35        12.53        69.11        51.35        21.63        18.21 
TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-EP-A12J TCGA-EP-A2KA 
       18.61        23.74        64.77        49.48        18.74        20.61 
TCGA-EP-A3JL TCGA-FV-A4ZQ TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL 
        9.96         0.39        22.13        19.53        25.25        20.42 
TCGA-G3-AAV5 TCGA-LG-A6GG TCGA-O8-A75V TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-ZS-A9CD 
        8.75        12.72        17.69        15.98         0.99        45.57 

$`XP GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       27.88       120.82        56.91        41.33        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        37.25        20.81        14.99         1.18         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
       13.02         8.61        10.78        10.59         0.66        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
       11.08         1.51        48.99        27.91        37.32        46.78 
TCGA-BC-A10T 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-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       18.48        44.81        13.45        36.66         0.66         0.07 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.19         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        11.47 
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        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81         7.66        70.06        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        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        26.83        30.51        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       23.05         1.45        35.67        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       75.65        76.41        55.40        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
        6.41        53.19         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
       61.68        13.64        14.20        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.25        18.15        20.98        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.17        21.83        18.90        15.72        25.08        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       23.64        25.78        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ 
       82.62        59.93        72.39        76.18        56.48        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        53.69        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         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        19.59         0.62        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       60.89        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33        81.73        13.68        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-A3CK TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A6UC 
       25.64         5.92        19.23        22.95        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       12.03         5.98         1.84        11.24         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.70         9.17         0.89         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.91        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
        3.72         2.14        11.84        13.38        24.36        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
        0.62        10.85        58.88        19.92        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
        0.76        17.59        19.76        16.44         1.71         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
       10.75        10.32        11.34        12.99        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        40.80        79.30        11.21 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.26              0.03 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           114.35            120.82 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           19.975            19.165 
[1] "0.3 - 114.3 (20.0)" "0.0 - 120.8 (19.2)"
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XP GAIN MUTATED        18       10         0          6          1          1
  XP GAIN WILD-TYPE     150       74         3         53          7          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XP GAIN MUTATED          0         0         0
  XP GAIN WILD-TYPE        3         1         2
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 18               150
  STAGE II                10                74
  STAGE III                0                 3
  STAGE IIIA               6                53
  STAGE IIIB               1                 7
  STAGE IIIC               1                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XP GAIN MUTATED      18  11   9   1
  XP GAIN WILD-TYPE   161  80  64  11
D40V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1              18               161
  T2                 11                80
  T3                  9                64
  T4                  1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    24   0
  XP GAIN WILD-TYPE 225   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     24    0
  XP GAIN WILD-TYPE  225    3
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              24               225
  1               0                 3
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    27   0
  XP GAIN WILD-TYPE 233   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     27    0
  XP GAIN WILD-TYPE  233    4
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              27               233
  1               0                 4
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    12  27
  XP GAIN WILD-TYPE 101 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     12   27
  XP GAIN WILD-TYPE  101  217
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              12               101
  MALE                27               217
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XP GAIN MUTATED                         0                       39
  XP GAIN WILD-TYPE                       2                      309
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XP GAIN MUTATED                                  0
  XP GAIN WILD-TYPE                                7
D40V8, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      39               309
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    34   3   0   1
  XP GAIN WILD-TYPE 281  12   1  18
D40V9, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              34               281
  R1               3                12
  R2               0                 1
  RX               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  1    16
  XP GAIN WILD-TYPE                                0   140
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                           1    19
  XP GAIN WILD-TYPE                        16   154
D40V10, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         16               140
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         19               154
[1] 4 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
  XP GAIN MUTATED     1  36
  XP GAIN WILD-TYPE  10 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1   36
  XP GAIN WILD-TYPE   10  293
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              36               293
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    40  15
  XQ GAIN WILD-TYPE 185  94
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               55               279 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               15                94 
$`XQ GAIN MUTATED`
TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-5R-AA1C 
       53.39        41.79        40.41        56.91        47.74        11.97 
TCGA-BC-A10U TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A69I TCGA-BW-A5NO TCGA-CC-5260 
       27.52         1.12         0.26        12.72         0.66         2.86 
TCGA-DD-A11A TCGA-DD-A39V TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NF TCGA-DD-A4NK 
        2.60        21.14        17.59        13.78        30.97        39.78 
TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACS 
       78.84        22.78       114.35        12.53        69.11        59.31 
TCGA-DD-AACT TCGA-DD-AAD2 TCGA-DD-AADO TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAE9 
       51.35        21.63        14.89        18.21        18.61        23.74 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-EP-A12J 
       79.07        89.69        64.77        65.39        49.48        18.74 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A3CG 
       20.61         9.96        22.85         0.39        53.79        22.13 
TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-K7-A6G5 
       19.53        25.25        20.42         9.17         8.75        16.83 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-O8-A75V TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-ZS-A9CD 
       12.72        18.38        17.69        15.98         0.99        45.57 
TCGA-ZS-A9CG 
       11.21 

$`XQ GAIN WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       23.80        63.75        83.24        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 
      120.82        41.33        18.25        11.74        37.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG 
       14.99         1.18         8.55        13.02         8.61        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
       10.59         0.66        11.08         1.51        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       23.34        69.57         5.03        44.42        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER 
       17.98        14.60        18.48        44.81        13.45        36.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         3.19         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
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        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        27.19        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 
        7.66        70.06        20.12       102.74       107.11         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        33.14        32.52        90.28        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E 
        0.30        80.75        23.93         9.30        23.05         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       35.67        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       55.40        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       14.20        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62         4.50        18.54        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.87        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB 
       19.99         4.64        21.17        21.83        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       25.08        16.37        23.64        25.78        50.33        35.08 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ 
       82.62        59.93        72.39        76.18        56.48        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       66.25        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A26S 
       13.15        13.41        13.35         1.84         0.20        19.99 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.33        81.73        13.68        51.06        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       58.49        14.86        21.53        25.64         5.92        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       22.95        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 
       11.24         8.55        11.80         9.70         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06         3.72         2.14        11.84        13.38        24.36 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
        0.62        10.85        58.88        19.92        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
        0.76        17.59        19.76        16.44         1.71         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
       10.75        10.32        11.34        12.99        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       12.99        40.80        79.30 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.26              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           114.35            120.82 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            20.61             19.04 
[1] "0.3 - 114.3 (20.6)" "0.0 - 120.8 (19.0)"
[1] "hr=" "1.4"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ GAIN MUTATED        31       15         0         10          2          1
  XQ GAIN WILD-TYPE     137       69         3         49          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ GAIN MUTATED          0         0         0
  XQ GAIN WILD-TYPE        3         1         2
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 31               137
  STAGE II                15                69
  STAGE III                0                 3
  STAGE IIIA              10                49
  STAGE IIIB               2                 6
  STAGE IIIC               1                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XQ GAIN MUTATED      31  16  12   2
  XQ GAIN WILD-TYPE   148  75  61  10
D41V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1              31               148
  T2                 16                75
  T3                 12                61
  T4                  2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    42   0
  XQ GAIN WILD-TYPE 207   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     42    0
  XQ GAIN WILD-TYPE  207    3
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              42               207
  1               0                 3
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    43   0
  XQ GAIN WILD-TYPE 217   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     43    0
  XQ GAIN WILD-TYPE  217    4
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              43               217
  1               0                 4
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    14  47
  XQ GAIN WILD-TYPE  99 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     14   47
  XQ GAIN WILD-TYPE   99  197
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              14                99
  MALE                47               197
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XQ GAIN MUTATED                         0                       61
  XQ GAIN WILD-TYPE                       2                      287
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XQ GAIN MUTATED                                  0
  XQ GAIN WILD-TYPE                                7
D41V8, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      61               287
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of 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    53   3   0   4
  XQ GAIN WILD-TYPE 262  12   1  15
D41V9, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              53               262
  R1               3                12
  R2               0                 1
  RX               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  1    25
  XQ GAIN WILD-TYPE                                0   131
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           4    29
  XQ GAIN WILD-TYPE                        13   144
D41V10, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         25               131
  BLACK OR AFRICAN AMERICAN                      4                13
  WHITE                                         29               144
[1] 4 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
  XQ GAIN MUTATED     1  57
  XQ GAIN WILD-TYPE  10 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   57
  XQ GAIN WILD-TYPE   10  272
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              57               272
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    51  23
  1P LOSS WILD-TYPE 174  86
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               74               260 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               23                86 
$`1P LOSS MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       24.89        41.33        18.25        11.74        13.02        10.78 
TCGA-5C-A9VH TCGA-BC-A10S TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 
       10.59        46.78        13.84        14.60         0.07         3.19 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
        0.10         0.13        79.73       113.00         7.33         0.46 
TCGA-DD-A1E9 TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A9 
       90.71        49.15        33.04        55.69         7.66        30.61 
TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACH TCGA-DD-AACN 
       30.15        29.56         9.30         0.53         6.41        42.81 
TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD1 TCGA-DD-AADA TCGA-DD-AADJ 
       13.64        51.52        46.82        18.54        40.54        35.05 
TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEK 
       14.89        19.30        18.25        18.15        18.61        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVZ TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       89.69        59.93        62.47        13.35         9.73        12.82 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
       13.41        13.35         0.20        19.59         0.62        22.85 
TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X 
       27.88         0.33        81.73        13.68        53.79        58.49 
TCGA-G3-A25Y TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-LG-A9QC 
       14.86        20.42        17.10         2.14        11.84        13.97 
TCGA-MI-A75G TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-WQ-A9G7 
       18.38        15.52        24.13         0.76        16.44         0.99 
TCGA-WQ-AB4B TCGA-ZP-A9D1 
       12.99         0.69 

$`1P LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H7 
       27.88       120.82        40.41        56.91        47.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-AAPD 
       20.81        14.99         1.18         8.55         8.61         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       11.97        11.08         1.51        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER 
       17.98        12.72        18.48        44.81        13.45        36.66 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.66         2.86         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11C 
        0.07        37.78        83.57        53.33         2.60        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        11.47 
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-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19         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-A4NA 
       20.12       102.74       107.11        13.78         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        90.28        30.97        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      114.35        13.48        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        63.48        12.00        15.42        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS 
        0.30         3.52        58.16        61.68        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       51.35        50.33         5.59        47.67         5.62         4.50 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB 
       21.63        42.58        44.22        22.09        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       34.49        20.91         0.39        29.52        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE2 
       66.67        15.58        18.21        18.87        18.25        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
       19.99         4.64        21.17        21.83        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       79.07        82.62        72.39        76.18        56.48        64.77 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       15.85        13.91         0.20         0.20        14.04        13.15 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        1.84        18.74        19.99        20.61         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        60.89        23.97        19.10         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
       12.03         0.03         0.39        51.06        28.27        30.74 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       25.25        22.95         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       20.75        17.06        16.83         3.72         2.14        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       24.36        12.72        12.03         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         0.62        10.85        58.88        19.92        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       21.01         3.09        21.04        19.33        19.04        15.39 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.59        19.76         1.71        15.98         7.04        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       10.32        11.34        24.85        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.21        23.57        24.43        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           113.00            120.82 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            16.77             19.99 
[1] "0.1 - 113.0 (16.8)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1"  
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P LOSS MUTATED        34       21         1         15          2          1
  1P LOSS WILD-TYPE     134       63         2         44          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P LOSS MUTATED          2         0         1
  1P LOSS WILD-TYPE        1         1         1
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 34               134
  STAGE II                21                63
  STAGE III                1                 2
  STAGE IIIA              15                44
  STAGE IIIB               2                 6
  STAGE IIIC               1                 6
  STAGE IV                 2                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1P LOSS MUTATED      37  22  21   1
  1P LOSS WILD-TYPE   142  69  52  11
D42V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1              37               142
  T2                 22                69
  T3                 21                52
  T4                  1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    57   1
  1P LOSS WILD-TYPE 192   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     57    1
  1P LOSS WILD-TYPE  192    2
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              57               192
  1               1                 2
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    66   3
  1P LOSS WILD-TYPE 194   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     66    3
  1P LOSS WILD-TYPE  194    1
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              66               194
  1               3                 1
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    30  51
  1P LOSS WILD-TYPE  83 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     30   51
  1P LOSS WILD-TYPE   83  193
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              30                83
  MALE                51               193
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1P LOSS MUTATED                         0                       78
  1P LOSS WILD-TYPE                       2                      270
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1P LOSS MUTATED                                  3
  1P LOSS WILD-TYPE                                4
D42V8, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      78               270
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    71   3   1   6
  1P LOSS WILD-TYPE 244  12   0  13
D42V9, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              71               244
  R1               3                12
  R2               1                 0
  RX               6                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0    39
  1P LOSS WILD-TYPE                                1   117
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           3    38
  1P LOSS WILD-TYPE                        14   135
D42V10, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         39               117
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         38               135
[1] 4 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
  1P LOSS MUTATED     3  75
  1P LOSS WILD-TYPE   8 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3   75
  1P LOSS WILD-TYPE    8  254
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              75               254
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    12   9
  1Q LOSS WILD-TYPE 213 100
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21               313 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               100 
$`1Q LOSS MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-BC-A10S TCGA-BC-A217 TCGA-CC-5258 
       24.89        18.25        11.74        46.78        13.84         0.07 
TCGA-CC-A3MB TCGA-DD-A11B TCGA-DD-A1EJ TCGA-DD-A3A1 TCGA-DD-AACH TCGA-DD-AACW 
        0.10         0.46        33.04         7.66         6.41        46.82 
TCGA-DD-AADW TCGA-DD-AAEK TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-ES-A2HS 
       19.30        35.08        13.41        13.35         0.20        22.85 
TCGA-FV-A4ZP TCGA-G3-A25U TCGA-UB-AA0U 
       81.73        53.79        10.75 

$`1Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       37.25        20.81        14.99         1.18         8.55        13.02 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.61        10.78        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
        1.51        48.99        27.91        37.32        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        44.42         0.26        22.36        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       12.72        18.48        44.81        13.45        36.66         0.66 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.19         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        11.47        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-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
       27.19        55.69         5.62        19.76        25.81        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        90.28        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        63.48        12.00        15.42        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX 
       14.20        59.31        51.35        51.52        50.33         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        18.87        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       21.17        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        23.64        25.78        50.33        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        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         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-EP-A12J 
       12.82         0.20        14.04        13.15         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        20.61        19.59         0.62         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        60.89        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38        12.03         0.03         0.33         0.39        13.68 
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-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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        11.24         8.55        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        11.84        13.38        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        0.62        10.85        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        3.09        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       24.13         0.76        17.59        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.98         7.04        10.32        11.34         0.99        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        13.55        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.07              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            81.73            120.82 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            13.84             19.53 
[1] "0.1 - 81.7 (13.8)"  "0.0 - 120.8 (19.5)"
[1] "hr=" "1.7"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q LOSS MUTATED         7        7         0          6          0          1
  1Q LOSS WILD-TYPE     161       77         3         53          8          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q LOSS MUTATED          0         0         0
  1Q LOSS WILD-TYPE        3         1         2
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  7               161
  STAGE II                 7                77
  STAGE III                0                 3
  STAGE IIIA               6                53
  STAGE IIIB               0                 8
  STAGE IIIC               1                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1Q LOSS MUTATED       8   7   7   0
  1Q LOSS WILD-TYPE   171  84  66  12
D43V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               8               171
  T2                  7                84
  T3                  7                66
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    14   1
  1Q LOSS WILD-TYPE 235   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14    1
  1Q LOSS WILD-TYPE  235    2
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              14               235
  1               1                 2
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    16   0
  1Q LOSS WILD-TYPE 244   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     16    0
  1Q LOSS WILD-TYPE  244    4
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              16               244
  1               0                 4
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     8  14
  1Q LOSS WILD-TYPE 105 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      8   14
  1Q LOSS WILD-TYPE  105  230
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               8               105
  MALE                14               230
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1Q LOSS MUTATED                         0                       21
  1Q LOSS WILD-TYPE                       2                      327
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1Q LOSS MUTATED                                  1
  1Q LOSS WILD-TYPE                                6
D43V8, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      21               327
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    18   2   0   2
  1Q LOSS WILD-TYPE 297  13   1  17
D43V9, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              18               297
  R1               2                13
  R2               0                 1
  RX               2                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0    11
  1Q LOSS WILD-TYPE                                1   145
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           0    10
  1Q LOSS WILD-TYPE                        17   163
D43V10, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11               145
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                         10               163
[1] 4 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
  1Q LOSS MUTATED     0  20
  1Q LOSS WILD-TYPE  11 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   20
  1Q LOSS WILD-TYPE   11  309
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              20               309
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    21   7
  2P LOSS WILD-TYPE 204 102
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               28               306 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7               102 
$`2P LOSS MUTATED`
TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Y TCGA-BC-A3KF TCGA-BC-A69H 
       20.81        13.02        10.78        23.34         0.26        14.60 
TCGA-BD-A3EP TCGA-DD-A11C TCGA-DD-A39Y TCGA-DD-AACE TCGA-DD-AACU TCGA-DD-AADI 
       13.45        21.76         5.62        63.48        51.52        35.67 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADW TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX 
       20.91        29.52        19.30        13.41         9.73         0.20 
TCGA-ED-A7PZ TCGA-FV-A3I1 TCGA-G3-A25S TCGA-G3-A5SM TCGA-G3-AAV7 TCGA-GJ-A9DB 
        0.20         8.12        13.68        17.10         3.02         2.20 
TCGA-KR-A7K2 TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-WQ-AB4B 
       11.84        15.39         0.76        12.99 

$`2P LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       47.74        18.25        11.74        37.25        14.99         1.18 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55         8.61        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        1.51        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 
       27.52        27.52         2.99        25.32         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I 
        5.03        44.42        13.84        22.36        17.98        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       18.48        44.81        36.66         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.19         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-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-A1EF 
       79.40        66.31        19.79        75.65        11.47        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        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        27.19        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        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        59.31        51.35        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ 
       13.97        40.47        39.52         3.78        37.64        35.05 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       34.49         0.39        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        18.87        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       20.98        18.61        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       23.74        18.90        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        49.48        53.69        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.91        13.35        12.82        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.59         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       60.89        23.97        19.10        27.88         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33        81.73         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        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       20.42         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
        8.55        11.80         9.70         9.17         0.89         8.75 
TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        2.14         1.02         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       16.83         3.72         2.14        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.97        12.03         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         0.62        10.85        58.88        19.92        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK 
       21.01         3.09        21.04        19.33        19.04        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       24.13        17.59        19.76        16.44         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 
        7.04        10.75        10.32        11.34         0.99        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       13.55        35.77        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        40.80        79.30        11.21 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.20              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            63.48            120.82 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           13.430            19.775 
[1] "0.2 - 63.5 (13.4)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P LOSS MUTATED        14       11         0          3          1          0
  2P LOSS WILD-TYPE     154       73         3         56          7          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P LOSS MUTATED          0         0         0
  2P LOSS WILD-TYPE        3         1         2
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 14               154
  STAGE II                11                73
  STAGE III                0                 3
  STAGE IIIA               3                56
  STAGE IIIB               1                 7
  STAGE IIIC               0                 7
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2P LOSS MUTATED      16  10   4   1
  2P LOSS WILD-TYPE   163  81  69  11
D44V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1              16               163
  T2                 10                81
  T3                  4                69
  T4                  1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    18   0
  2P LOSS WILD-TYPE 231   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     18    0
  2P LOSS WILD-TYPE  231    3
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              18               231
  1               0                 3
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    24   0
  2P LOSS WILD-TYPE 236   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     24    0
  2P LOSS WILD-TYPE  236    4
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              24               236
  1               0                 4
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7  24
  2P LOSS WILD-TYPE 106 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7   24
  2P LOSS WILD-TYPE  106  220
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7               106
  MALE                24               220
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2P LOSS MUTATED                         0                       30
  2P LOSS WILD-TYPE                       2                      318
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2P LOSS MUTATED                                  1
  2P LOSS WILD-TYPE                                6
D44V8, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      30               318
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    26   1   0   4
  2P LOSS WILD-TYPE 289  14   1  15
D44V9, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              26               289
  R1               1                14
  R2               0                 1
  RX               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0    15
  2P LOSS WILD-TYPE                                1   141
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           2    14
  2P LOSS WILD-TYPE                        15   159
D44V10, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15               141
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         14               159
[1] 4 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
  2P LOSS MUTATED     0  29
  2P LOSS WILD-TYPE  11 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   29
  2P LOSS WILD-TYPE   11  300
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              29               300
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    24   8
  2Q LOSS WILD-TYPE 201 101
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               32               302 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8               101 
$`2Q LOSS MUTATED`
TCGA-2Y-A9GU TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Y TCGA-BC-A3KF TCGA-BD-A3EP 
       63.75        13.02        10.78        23.34         0.26        13.45 
TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A39Y TCGA-DD-A4NJ TCGA-DD-A73B TCGA-DD-AACE 
       83.57        21.76         5.62        30.51         9.30        63.48 
TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE6 
       35.67        20.91        29.52        19.30        20.98         4.64 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-FV-A3I1 
       13.41         9.73         0.20         0.20        14.04         8.12 
TCGA-G3-A5SM TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A7SH TCGA-T1-A6J8 
       17.10         3.02         2.20        11.84        15.39         0.76 
TCGA-UB-A7MF TCGA-WQ-AB4B 
        7.04        12.99 

$`2Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55         8.61        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        1.51        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 
       27.52        27.52         2.99        25.32         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        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       12.72        18.48        44.81        36.66         0.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.19         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 
        0.07         0.10         0.13        79.73        37.78        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-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-A1EF 
       79.40        66.31        19.79        75.65        11.47        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        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        27.19        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        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        26.83        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52         3.78        37.64        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 
       18.21        18.87        18.25        18.25        18.15        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
       19.99        21.17        21.83        23.74        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       25.08        16.37        23.64        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       53.69        12.69        15.85        13.91        13.35        12.82 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        20.61        19.59         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38        12.03         0.03         0.33        81.73         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       13.68        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-A6UC TCGA-G3-A7M6 
       19.23        25.25        22.95        20.42         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        5.98         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        9.17         0.89         8.75         2.14         1.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.91        20.75        17.06        16.83         3.72         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        19.92        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.33        19.04        15.52        24.13        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       16.44         1.71        15.98        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99        24.85        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.20              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            83.57            120.82 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           13.215            19.775 
[1] "0.2 - 83.6 (13.2)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q LOSS MUTATED        16       10         0          7          1          0
  2Q LOSS WILD-TYPE     152       74         3         52          7          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q LOSS MUTATED          0         0         0
  2Q LOSS WILD-TYPE        3         1         2
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 16               152
  STAGE II                10                74
  STAGE III                0                 3
  STAGE IIIA               7                52
  STAGE IIIB               1                 7
  STAGE IIIC               0                 7
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2Q LOSS MUTATED      17  10   8   1
  2Q LOSS WILD-TYPE   162  81  65  11
D45V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1              17               162
  T2                 10                81
  T3                  8                65
  T4                  1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    23   0
  2Q LOSS WILD-TYPE 226   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     23    0
  2Q LOSS WILD-TYPE  226    3
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              23               226
  1               0                 3
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    28   0
  2Q LOSS WILD-TYPE 232   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     28    0
  2Q LOSS WILD-TYPE  232    4
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              28               232
  1               0                 4
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    10  26
  2Q LOSS WILD-TYPE 103 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     10   26
  2Q LOSS WILD-TYPE  103  218
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              10               103
  MALE                26               218
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2Q LOSS MUTATED                         0                       35
  2Q LOSS WILD-TYPE                       2                      313
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2Q LOSS MUTATED                                  1
  2Q LOSS WILD-TYPE                                6
D45V8, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      35               313
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    31   0   0   5
  2Q LOSS WILD-TYPE 284  15   1  14
D45V9, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              31               284
  R1               0                15
  R2               0                 1
  RX               5                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0    18
  2Q LOSS WILD-TYPE                                1   138
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           2    16
  2Q LOSS WILD-TYPE                        15   157
D45V10, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         18               138
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         16               157
[1] 4 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
  2Q LOSS MUTATED     1  32
  2Q LOSS WILD-TYPE  10 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   32
  2Q LOSS WILD-TYPE   10  297
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              32               297
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    32  12
  3P LOSS WILD-TYPE 193  97
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               44               290 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12                97 
$`3P LOSS MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       24.89        56.91        41.33        18.25        13.02        10.78 
TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A112 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB 
        0.66        10.13         5.03         4.24         0.07         0.10 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1E9 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NI 
       79.73       113.00        90.71        30.61        33.14        26.83 
TCGA-DD-A4NO TCGA-DD-AACO TCGA-DD-AADO TCGA-DD-AADY TCGA-DD-AAVQ TCGA-DD-AAVU 
       73.81        61.68        14.89        18.25        89.69        72.39 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A97K TCGA-FV-A3I0 
        9.73         0.20         0.20        13.41         0.20        27.88 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K7 
       51.06        58.49        11.80         2.14        11.84        13.38 
TCGA-LG-A9QC TCGA-MR-A8JO TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-WQ-AB4B 
       13.97        10.85        16.44         1.71         7.04        12.99 
TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.69        40.80 

$`3P LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       27.88       120.82        40.41        47.74        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        14.99         1.18         8.55         8.61        10.59 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       11.97        11.08         1.51        48.99        27.91        37.32 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57        44.42        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       17.98        14.60        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       36.66         0.66         0.07         2.86         3.19         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        3.32         0.10         0.13        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
        7.33         2.60         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        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        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
        0.36        32.52        90.28        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       58.16        42.81        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        18.87        19.30        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       18.90        15.72        25.08        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       50.33        35.08        79.07        82.62        59.93        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J 
       12.82        14.04        13.15        13.35         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        20.61        19.59         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       22.85        14.40        60.89        23.97        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38        12.03         0.03         0.33        81.73         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 
       20.75        17.06        16.83         3.72         2.14        24.36 
TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       12.72        12.03         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71         0.62        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        3.09        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U 
       24.13         0.76        17.59        19.76        15.98        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       10.32        11.34         0.99        24.85        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           113.00            120.82 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            13.69             19.76 
[1] "0.1 - 113.0 (13.7)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P LOSS MUTATED        13       15         0         14          2          2
  3P LOSS WILD-TYPE     155       69         3         45          6          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P LOSS MUTATED          0         0         1
  3P LOSS WILD-TYPE        3         1         1
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 13               155
  STAGE II                15                69
  STAGE III                0                 3
  STAGE IIIA              14                45
  STAGE IIIB               2                 6
  STAGE IIIC               2                 5
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3P LOSS MUTATED      14  16  17   3
  3P LOSS WILD-TYPE   165  75  56   9
D46V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              14               165
  T2                 16                75
  T3                 17                56
  T4                  3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    34   1
  3P LOSS WILD-TYPE 215   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     34    1
  3P LOSS WILD-TYPE  215    2
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              34               215
  1               1                 2
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    35   1
  3P LOSS WILD-TYPE 225   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     35    1
  3P LOSS WILD-TYPE  225    3
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              35               225
  1               1                 3
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    19  31
  3P LOSS WILD-TYPE  94 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     19   31
  3P LOSS WILD-TYPE   94  213
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              19                94
  MALE                31               213
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3P LOSS MUTATED                         1                       45
  3P LOSS WILD-TYPE                       1                      303
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3P LOSS MUTATED                                  4
  3P LOSS WILD-TYPE                                3
D46V8, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      45               303
  HEPATOCHOLANGIOCARCINOMA (MIXED)               4                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    47   0   0   3
  3P LOSS WILD-TYPE 268  15   1  16
D46V9, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              47               268
  R1               0                15
  R2               0                 1
  RX               3                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0    22
  3P LOSS WILD-TYPE                                1   134
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           2    26
  3P LOSS WILD-TYPE                        15   147
D46V10, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         22               134
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         26               147
[1] 4 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
  3P LOSS MUTATED     1  46
  3P LOSS WILD-TYPE  10 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   46
  3P LOSS WILD-TYPE   10  283
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              46               283
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    24   8
  3Q LOSS WILD-TYPE 201 101
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               32               302 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8               101 
$`3Q LOSS MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A112 
       24.89        41.33        18.25        13.02        10.78         5.03 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1E9 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NO 
       79.73       113.00        90.71        33.14        26.83        73.81 
TCGA-DD-AACO TCGA-DD-AADO TCGA-DD-AADY TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-ED-A66Y 
       61.68        14.89        18.25        89.69        72.39         9.73 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-G3-AAV1 TCGA-G3-AAV6 
        0.20        13.41         1.84         0.20        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MR-A8JO TCGA-UB-A7MC TCGA-WQ-AB4B 
       11.84        13.38        13.97        10.85        16.44        12.99 
TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.69        40.80 

$`3Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H6 
       27.88       120.82        40.41        56.91        47.74        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I 
       37.25        20.81        14.99         1.18         8.55         8.61 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.59         0.66        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       18.48        44.81        13.45        36.66         0.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.19         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-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
        7.33         2.60         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        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        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        30.61        32.52        90.28        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        39.78        56.25        29.56       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        3.52        58.16        42.81        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91         0.39        29.52        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        18.87        19.30        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       20.98        18.61        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       23.74        18.90        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        35.08        79.07        82.62        59.93 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
       13.35         0.20        12.82        14.04        13.15        13.35 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       81.73         0.39        13.68        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        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
        8.55         9.70         9.17         0.89         8.75         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD 
       16.83         3.72         2.14        24.36        12.72        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
        9.57        16.67        18.38        12.85        20.71         0.62 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        19.92        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       19.33        19.04        15.39        15.52        24.13         0.76 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.59        19.76         1.71        15.98         7.04        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       10.32        11.34         0.99        24.85        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.20              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           113.00            120.82 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           14.430            19.675 
[1] "0.2 - 113.0 (14.4)" "0.0 - 120.8 (19.7)"
[1] "hr=" "1.5"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q LOSS MUTATED        11       11         0         10          2          2
  3Q LOSS WILD-TYPE     157       73         3         49          6          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q LOSS MUTATED          0         0         0
  3Q LOSS WILD-TYPE        3         1         2
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 11               157
  STAGE II                11                73
  STAGE III                0                 3
  STAGE IIIA              10                49
  STAGE IIIB               2                 6
  STAGE IIIC               2                 5
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3Q LOSS MUTATED      12  12  12   2
  3Q LOSS WILD-TYPE   167  79  61  10
D47V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1              12               167
  T2                 12                79
  T3                 12                61
  T4                  2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    26   1
  3Q LOSS WILD-TYPE 223   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     26    1
  3Q LOSS WILD-TYPE  223    2
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              26               223
  1               1                 2
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    28   0
  3Q LOSS WILD-TYPE 232   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     28    0
  3Q LOSS WILD-TYPE  232    4
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              28               232
  1               0                 4
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    14  24
  3Q LOSS WILD-TYPE  99 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     14   24
  3Q LOSS WILD-TYPE   99  220
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              14                99
  MALE                24               220
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3Q LOSS MUTATED                         1                       35
  3Q LOSS WILD-TYPE                       1                      313
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3Q LOSS MUTATED                                  2
  3Q LOSS WILD-TYPE                                5
D47V8, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      35               313
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    36   0   0   2
  3Q LOSS WILD-TYPE 279  15   1  17
D47V9, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              36               279
  R1               0                15
  R2               0                 1
  RX               2                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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    17
  3Q LOSS WILD-TYPE                                1   139
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           1    20
  3Q LOSS WILD-TYPE                        16   153
D47V10, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17               139
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         20               153
[1] 4 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
  3Q LOSS MUTATED     1  34
  3Q LOSS WILD-TYPE  10 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   34
  3Q LOSS WILD-TYPE   10  295
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              34               295
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    59  29
  4P LOSS WILD-TYPE 166  80
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               88               246 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               29                80 
$`4P LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-AAPD 
       23.80        24.89        41.33        13.02        10.78         0.66 
TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       23.34         5.03        13.84        22.36        17.98        14.60 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 
       13.45         0.66         0.13        79.73        37.78         7.33 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 
        6.02        33.04        13.64        55.69         5.62        30.61 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACE 
       26.83        30.51        29.56         0.53        76.41        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACY 
       12.00        15.42        42.81        13.64        51.52        47.67 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADR 
       44.22        40.08        13.97        40.47        20.91        66.67 
TCGA-DD-AADV TCGA-DD-AAE0 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK 
       18.87        18.25        21.83        18.90        25.08        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVW TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY 
       89.69        72.39        76.18        13.41        13.35        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ 
        0.20        14.04         1.84        19.59         0.62        23.97 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A7M9 
        0.33        81.73        13.68        53.79        58.49         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-K7-A5RG TCGA-KR-A7K2 
       11.24        11.80         0.89         2.14        17.06        11.84 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MI-A75G TCGA-PD-A5DF TCGA-RC-A7SB TCGA-RC-A7SK 
       13.38        13.97        18.38        21.01        19.33        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-AB4B 
       24.13        19.76        16.44        15.98         7.04        12.99 
TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       13.55        24.43        40.80        79.30 

$`4P LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
      120.82        40.41        56.91        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I 
       37.25        20.81        14.99         1.18         8.55         8.61 
TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
       10.59        11.97        11.08         1.51        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       37.32        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69I 
       25.32         1.12        69.57        44.42         0.26        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       18.48        44.81        36.66         0.07         2.86         3.19 
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-A1EK TCGA-DD-A39V 
       11.47        12.95        45.11        49.15        18.35        21.14 
TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        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        90.28        30.97        30.15        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
      114.35        13.48        11.41        75.65        55.40        12.53 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW 
       61.68        14.20        59.31        51.35        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       22.09        40.54        40.83        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.67        35.05        34.49         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       15.06        14.33        15.58        18.21        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.15        20.98        18.61        19.99         4.64        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        16.37        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       79.07        82.62        59.93        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        49.48        53.69        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       13.91         9.73         0.20        13.15        13.41        13.35 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        18.74        19.99        20.61         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        60.89        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V 
        6.38        12.03         0.03         0.39        51.06        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        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
        7.76        12.03         5.98         8.55         9.70         9.17 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG 
       20.75        16.83         3.72         2.14        24.36        12.72 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 
       10.85        58.88        19.92        17.69         3.09        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U 
       19.04        15.39         0.76        17.59         1.71        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       10.32        11.34         0.99        24.85        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.21        23.57         0.69        12.99        45.57        11.21 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            89.69            120.82 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           18.315            19.775 
[1] "0.1 - 89.7 (18.3)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P LOSS MUTATED        39       30         0         20          3          2
  4P LOSS WILD-TYPE     129       54         3         39          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P LOSS MUTATED          3         1         1
  4P LOSS WILD-TYPE        0         0         1
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 39               129
  STAGE II                30                54
  STAGE III                0                 3
  STAGE IIIA              20                39
  STAGE IIIB               3                 5
  STAGE IIIC               2                 5
  STAGE IV                 3                 0
  STAGE IVA                1                 0
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4P LOSS MUTATED      41  33  24   4
  4P LOSS WILD-TYPE   138  58  49   8
D48V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              41               138
  T2                 33                58
  T3                 24                49
  T4                  4                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    68   2
  4P LOSS WILD-TYPE 181   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     68    2
  4P LOSS WILD-TYPE  181    1
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              68               181
  1               2                 1
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    77   3
  4P LOSS WILD-TYPE 183   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     77    3
  4P LOSS WILD-TYPE  183    1
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              77               183
  1               3                 1
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    26  76
  4P LOSS WILD-TYPE  87 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     26   76
  4P LOSS WILD-TYPE   87  168
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              26                87
  MALE                76               168
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4P LOSS MUTATED                         0                      100
  4P LOSS WILD-TYPE                       2                      248
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4P LOSS MUTATED                                  2
  4P LOSS WILD-TYPE                                5
D48V8, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     100               248
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED    92   3   1   5
  4P LOSS WILD-TYPE 223  12   0  14
D48V9, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              92               223
  R1               3                12
  R2               1                 0
  RX               5                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0    53
  4P LOSS WILD-TYPE                                1   103
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           8    40
  4P LOSS WILD-TYPE                         9   133
D48V10, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         53               103
  BLACK OR AFRICAN AMERICAN                      8                 9
  WHITE                                         40               133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     5  94
  4P LOSS WILD-TYPE   6 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5   94
  4P LOSS WILD-TYPE    6  235
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 6
  NOT HISPANIC OR LATINO              94               235
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    86  39
  4Q LOSS WILD-TYPE 139  70
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              125               209 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               39                70 
$`4Q LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-2Y-A9HA 
       23.80        24.89        56.91        41.33        20.81         1.18 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10T TCGA-BC-A10Y 
       13.02        10.78        10.59         0.66        27.52        23.34 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        13.84         0.26        22.36        17.98        14.60 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
       13.45         0.66         0.10         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A1EH 
       37.78        53.33         7.33         2.60        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 
        6.02        33.04        13.64        55.69         5.62        30.61 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B 
       30.15        26.83        30.51        29.56        73.81         9.30 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
        0.53        76.41        55.40        63.48        12.00        15.42 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU 
        3.52        58.16        42.81        13.64        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB 
       50.33        46.82         5.62        44.22        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP 
       13.97        40.47        35.67        20.91        14.89        15.06 
TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 
       66.67        18.87        18.25        18.25        18.15         4.64 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS 
       21.83        18.90        25.08        35.08        89.69        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAW0 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       72.39        76.18        66.25        13.35        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC 
       14.04        13.15        13.35         0.20        19.59         0.62 
TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X 
       23.97         8.12         0.33        81.73        13.68        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 
       14.86        21.53        25.25        17.10         1.84        11.80 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 
        0.89         2.14         3.02        17.06        11.84        13.38 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK 
       12.72        13.97        18.38        19.33        15.39        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       24.13         0.76        19.76        16.44        15.98         7.04 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
        0.99        12.99        13.55        24.43        40.80 

$`4Q LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
      120.82        40.41        47.74        18.25        11.74        37.25 
TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       14.99         8.55         8.61        11.97        11.08         1.51 
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-A69I 
        2.99        25.32         1.12        69.57        44.42        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       18.48        44.81        36.66         0.07         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 
        3.39         4.24         3.32         0.07        83.57       113.00 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EK TCGA-DD-A39V 
       19.79        75.65        11.47        12.95        18.35        21.14 
TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        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-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       32.52        90.28        30.97        39.78        56.25       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       12.26         0.30        80.75        78.84        23.93        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 
       22.78         1.45        35.67       114.35        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       75.65        12.53         6.41        53.19        69.11         0.30 
TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       61.68        14.20        51.35         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADE 
       18.54        21.63        42.58        22.09        40.54        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN 
        3.78        37.64        35.05        34.49         0.39        29.52 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 
       14.33        15.58        18.21        19.30        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG 
       19.99        21.17        23.74        15.72        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY 
       25.78        50.33        79.07        82.62        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       62.47        65.39        49.48        53.69        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A8O6 
       15.85        13.91         9.73         0.20        13.41         1.84 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       18.74        19.99        20.61         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        60.89        19.10        27.88         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.39        51.06        53.79        28.27        30.74 
TCGA-G3-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        22.95 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.42         7.76        12.03         5.98        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        9.70         9.17         8.75         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 
       37.91        20.75        16.83         3.72         2.14        24.36 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        19.92        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-UB-AA0V 
       21.04        19.04        17.59         1.71        10.75        10.32 
TCGA-WJ-A86L TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       11.34        24.85        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
        0.69        12.99        45.57        79.30        11.21 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.10              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            89.69            120.82 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            17.98             19.99 
[1] "0.1 - 89.7 (18.0)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED        60       38         1         26          4          2
  4Q LOSS WILD-TYPE     108       46         2         33          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q LOSS MUTATED          3         1         1
  4Q LOSS WILD-TYPE        0         0         1
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 60               108
  STAGE II                38                46
  STAGE III                1                 2
  STAGE IIIA              26                33
  STAGE IIIB               4                 4
  STAGE IIIC               2                 5
  STAGE IV                 3                 0
  STAGE IVA                1                 0
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4Q LOSS MUTATED      64  40  33   5
  4Q LOSS WILD-TYPE   115  51  40   7
D49V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              64               115
  T2                 40                51
  T3                 33                40
  T4                  5                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   101   2
  4Q LOSS WILD-TYPE 148   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    101    2
  4Q LOSS WILD-TYPE  148    1
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             101               148
  1               2                 1
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   113   3
  4Q LOSS WILD-TYPE 147   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    113    3
  4Q LOSS WILD-TYPE  147    1
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             113               147
  1               3                 1
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    40 102
  4Q LOSS WILD-TYPE  73 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     40  102
  4Q LOSS WILD-TYPE   73  142
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              40                73
  MALE               102               142
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4Q LOSS MUTATED                         0                      139
  4Q LOSS WILD-TYPE                       2                      209
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4Q LOSS MUTATED                                  3
  4Q LOSS WILD-TYPE                                4
D49V8, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     139               209
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED   131   4   1   6
  4Q LOSS WILD-TYPE 184  11   0  13
D49V9, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             131               184
  R1               4                11
  R2               1                 0
  RX               6                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0    79
  4Q LOSS WILD-TYPE                                1    77
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           9    54
  4Q LOSS WILD-TYPE                         8   119
D49V10, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         79                77
  BLACK OR AFRICAN AMERICAN                      9                 8
  WHITE                                         54               119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     5 133
  4Q LOSS WILD-TYPE   6 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5  133
  4Q LOSS WILD-TYPE    6  196
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 6
  NOT HISPANIC OR LATINO             133               196
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    16   6
  5P LOSS WILD-TYPE 209 103
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               22               312 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6               103 
$`5P LOSS MUTATED`
TCGA-5C-AAPD TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-A3M9 TCGA-DD-A11A TCGA-DD-A1EH 
        0.66        46.78         0.07         0.10         2.60        49.15 
TCGA-DD-A1EJ TCGA-DD-A4NB TCGA-DD-AACS TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADG 
       33.04        32.52        59.31        40.83        40.47        37.64 
TCGA-DD-AADI TCGA-DD-AADW TCGA-DD-AAVQ TCGA-ED-A97K TCGA-ES-A2HS TCGA-FV-A496 
       35.67        19.30        89.69         0.20        22.85         0.33 
TCGA-G3-A25S TCGA-G3-A7M9 TCGA-G3-AAV6 TCGA-G3-AAV7 
       13.68         1.84         2.14         3.02 

$`5P LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       11.97        11.08         1.51        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       22.36        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45        36.66         0.66         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65        11.47        12.95        45.11         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        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-A4ND 
      107.11        13.78         0.36        30.61        33.14        90.28 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU 
       42.81        61.68        13.64        14.20        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADK 
       40.54        13.97        39.52         3.78        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        18.87        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.15        20.98        18.61        19.99         4.64        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.83        23.74        18.90        15.72        25.08        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR 
       23.64        25.78        50.33        35.08        79.07        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        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         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        8.12         6.38        12.03         0.03        81.73         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-A7M6 
       25.25        22.95        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        5.98        11.24         8.55        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        0.89         8.75         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83         3.72         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        19.92        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       19.33        19.04        15.39        15.52        24.13         0.76 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       17.59        19.76        16.44         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       10.75        10.32        11.34         0.99        12.99        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       13.55        35.77        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        40.80        79.30        11.21 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.07              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            89.69            120.82 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           21.075            19.165 
[1] "0.1 - 89.7 (21.1)"  "0.0 - 120.8 (19.2)"
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P LOSS MUTATED        11        5         1          7          1          1
  5P LOSS WILD-TYPE     157       79         2         52          7          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P LOSS MUTATED          0         0         0
  5P LOSS WILD-TYPE        3         1         2
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 11               157
  STAGE II                 5                79
  STAGE III                1                 2
  STAGE IIIA               7                52
  STAGE IIIB               1                 7
  STAGE IIIC               1                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5P LOSS MUTATED      12   5  10   0
  5P LOSS WILD-TYPE   167  86  63  12
D50V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              12               167
  T2                  5                86
  T3                 10                63
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    22   1
  5P LOSS WILD-TYPE 227   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     22    1
  5P LOSS WILD-TYPE  227    2
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              22               227
  1               1                 2
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    24   0
  5P LOSS WILD-TYPE 236   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     24    0
  5P LOSS WILD-TYPE  236    4
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              24               236
  1               0                 4
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     6  21
  5P LOSS WILD-TYPE 107 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6   21
  5P LOSS WILD-TYPE  107  223
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               6               107
  MALE                21               223
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5P LOSS MUTATED                         1                       24
  5P LOSS WILD-TYPE                       1                      324
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5P LOSS MUTATED                                  2
  5P LOSS WILD-TYPE                                5
D50V8, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      24               324
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    25   1   0   1
  5P LOSS WILD-TYPE 290  14   1  18
D50V9, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              25               290
  R1               1                14
  R2               0                 1
  RX               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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    17
  5P LOSS WILD-TYPE                                1   139
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           1     9
  5P LOSS WILD-TYPE                        16   164
D50V10, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17               139
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                          9               164
[1] 4 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
  5P LOSS MUTATED     0  27
  5P LOSS WILD-TYPE  11 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   27
  5P LOSS WILD-TYPE   11  302
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              27               302
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    19  12
  5Q LOSS WILD-TYPE 206  97
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               31               303 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               12                97 
$`5Q LOSS MUTATED`
TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A10S TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A11A 
        0.66        10.13        46.78         4.24         0.10         2.60 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A4NB TCGA-DD-AACS TCGA-DD-AAD8 
       12.95        49.15        33.04        32.52        59.31        40.08 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADW TCGA-DD-AAVQ TCGA-ED-A8O6 
       40.83        40.47        35.67        19.30        89.69         1.84 
TCGA-ED-A97K TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        0.20        22.85        27.88         0.33        81.73        13.68 
TCGA-G3-A25X TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-UB-A7MB 
       58.49        12.03         1.84         2.14         3.02        19.76 
TCGA-UB-A7MF 
        7.04 

$`5Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       11.97        11.08         1.51        48.99        27.91        37.32 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       69.57         5.03        44.42        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       17.98        14.60        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       36.66         0.66         0.07         2.86         3.19         3.39 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         7.33         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       11.47        45.11         6.02        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        30.61        33.14        90.28        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADE 
       42.58        44.22        22.09        40.54        13.97        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
        3.78        37.64        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        18.87        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       18.90        15.72        25.08        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        35.08        79.07        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.15        13.41        13.35        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       19.59         0.62         9.96        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10         8.12         6.38        12.03         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       25.25        22.95        20.42        17.10         7.76         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        8.75         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83         3.72         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       18.38        12.85        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       19.92        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.04        15.39        15.52        24.13         0.76        17.59 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       16.44         1.71        15.98        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        0.99        12.99        24.85        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.10              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            89.69            120.82 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            19.30             19.23 
[1] "0.1 - 89.7 (19.3)"  "0.0 - 120.8 (19.2)"
[1] "hr=" "1.3"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED        14        7         1         12          1          1
  5Q LOSS WILD-TYPE     154       77         2         47          7          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q LOSS MUTATED          0         0         0
  5Q LOSS WILD-TYPE        3         1         2
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 14               154
  STAGE II                 7                77
  STAGE III                1                 2
  STAGE IIIA              12                47
  STAGE IIIB               1                 7
  STAGE IIIC               1                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5Q LOSS MUTATED      15   7  16   0
  5Q LOSS WILD-TYPE   164  84  57  12
D51V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              15               164
  T2                  7                84
  T3                 16                57
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    27   1
  5Q LOSS WILD-TYPE 222   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     27    1
  5Q LOSS WILD-TYPE  222    2
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              27               222
  1               1                 2
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    31   0
  5Q LOSS WILD-TYPE 229   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     31    0
  5Q LOSS WILD-TYPE  229    4
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              31               229
  1               0                 4
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    12  26
  5Q LOSS WILD-TYPE 101 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     12   26
  5Q LOSS WILD-TYPE  101  218
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              12               101
  MALE                26               218
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5Q LOSS MUTATED                         1                       34
  5Q LOSS WILD-TYPE                       1                      314
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5Q LOSS MUTATED                                  3
  5Q LOSS WILD-TYPE                                4
D51V8, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      34               314
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    35   2   0   1
  5Q LOSS WILD-TYPE 280  13   1  18
D51V9, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              35               280
  R1               2                13
  R2               0                 1
  RX               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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    21
  5Q LOSS WILD-TYPE                                1   135
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           1    16
  5Q LOSS WILD-TYPE                        16   157
D51V10, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         21               135
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         16               157
[1] 4 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
  5Q LOSS MUTATED     0  38
  5Q LOSS WILD-TYPE  11 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   38
  5Q LOSS WILD-TYPE   11  291
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              38               291
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    16  10
  6P LOSS WILD-TYPE 209  99
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               26               308 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10                99 
$`6P LOSS MUTATED`
TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-A3M9 TCGA-DD-A118 
      120.82        56.91        17.98        12.72         0.10       113.00 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF 
        2.60        21.76        90.71        19.79        11.47        12.95 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39Z TCGA-DD-A4NH TCGA-DD-A4NK 
        6.02        33.04        18.35        19.76        30.15        39.78 
TCGA-DD-AAEG TCGA-DD-AAVU TCGA-ED-A66Y TCGA-G3-AAV6 TCGA-UB-A7MB TCGA-UB-A7ME 
       23.64        72.39         9.73         2.14        19.76        15.98 
TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.69        40.80 

$`6P LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       24.89        27.88        40.41        41.33        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        37.25        20.81        14.99         1.18         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
       13.02         8.61        10.78        10.59         0.66        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       11.08         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER 
       22.36        14.60        18.48        44.81        13.45        36.66 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         0.07         2.86         3.19         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-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA 
       83.57        53.33         7.33         0.46        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V 
       66.31        75.65        45.11        49.15        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        55.69         5.62        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI 
       30.61        33.14        32.52        90.28        30.97        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       14.33        66.67        15.58        18.21        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        21.17        21.83        23.74        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        16.37        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       89.69        82.62        59.93        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        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        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        9.96        11.93        22.85        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        81.73         0.39        13.68        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        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83         3.72         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        19.92        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       19.33        19.04        15.39        15.52        24.13         0.76 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       17.59        16.44         1.71         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       11.34         0.99        12.99        24.85        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.10              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           120.82            114.35 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           19.760            19.165 
[1] "0.1 - 120.8 (19.8)" "0.0 - 114.3 (19.2)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P LOSS MUTATED        10        5         0          8          1          1
  6P LOSS WILD-TYPE     158       79         3         51          7          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P LOSS MUTATED          0         0         1
  6P LOSS WILD-TYPE        3         1         1
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 10               158
  STAGE II                 5                79
  STAGE III                0                 3
  STAGE IIIA               8                51
  STAGE IIIB               1                 7
  STAGE IIIC               1                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6P LOSS MUTATED      12   5   9   1
  6P LOSS WILD-TYPE   167  86  64  11
D52V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1              12               167
  T2                  5                86
  T3                  9                64
  T4                  1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    20   1
  6P LOSS WILD-TYPE 229   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     20    1
  6P LOSS WILD-TYPE  229    2
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              20               229
  1               1                 2
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    21   1
  6P LOSS WILD-TYPE 239   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     21    1
  6P LOSS WILD-TYPE  239    3
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              21               239
  1               1                 3
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    14  13
  6P LOSS WILD-TYPE  99 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     14   13
  6P LOSS WILD-TYPE   99  231
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              14                99
  MALE                13               231
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6P LOSS MUTATED                         0                       27
  6P LOSS WILD-TYPE                       2                      321
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6P LOSS MUTATED                                  0
  6P LOSS WILD-TYPE                                7
D52V8, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      27               321
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of 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    25   1   0   1
  6P LOSS WILD-TYPE 290  14   1  18
D52V9, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              25               290
  R1               1                14
  R2               0                 1
  RX               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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     7
  6P LOSS WILD-TYPE                                1   149
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           1    18
  6P LOSS WILD-TYPE                        16   155
D52V10, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7               149
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         18               155
[1] 4 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
  6P LOSS MUTATED     1  24
  6P LOSS WILD-TYPE  10 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   24
  6P LOSS WILD-TYPE   10  305
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              24               305
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    55  30
  6Q LOSS WILD-TYPE 170  79
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               85               249 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               30                79 
$`6Q LOSS MUTATED`
TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-4R-AA8I TCGA-5R-AA1C 
      120.82        56.91        37.25        20.81         8.61        11.97 
TCGA-5R-AAAM TCGA-BC-A10Q TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5260 
        1.51        37.32         0.26        17.98        12.72         2.86 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 
        0.10         0.07       113.00         2.60        21.76        90.71 
TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       19.79        11.47        12.95         6.02        33.04        18.35 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NH 
       55.69        19.76         7.66         0.36        33.14        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NS TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC8 
       30.51        39.78        80.75         1.45        13.48         0.53 
TCGA-DD-AACE TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AAD3 
       63.48         6.41        53.19        13.64        51.52        42.58 
TCGA-DD-AAD8 TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADP TCGA-DD-AADV TCGA-DD-AADY 
       40.08        34.49        20.91        15.06        18.87        18.25 
TCGA-DD-AAE2 TCGA-DD-AAE9 TCGA-DD-AAEG TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVY 
       20.98        23.74        23.64        59.93        72.39        64.77 
TCGA-DD-AAW3 TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       53.69         9.73         0.20        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR 
        0.20        18.74        11.93        22.85        60.89        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SL 
       27.88         6.38        81.73        51.06        58.49        20.42 
TCGA-G3-A6UC TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5N0 TCGA-MI-A75E 
        7.76         9.17         0.89         2.14        37.91        16.67 
TCGA-MI-A75I TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-ZP-A9D1 
       20.71         0.76        19.76        15.98        10.75         0.69 
TCGA-ZS-A9CE 
       40.80 

$`6Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       24.89        27.88        40.41        41.33        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       11.74        14.99         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
       10.59         0.66        11.08        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42        13.84        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       14.60        18.48        44.81        13.45        36.66         0.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB 
        0.07         3.19         3.39         4.24         3.32         0.10 
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-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EG 
        0.46        51.29        79.40        66.31        75.65        45.11 
TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A3A0 
       49.15        13.64        21.14        27.19         5.62        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NL 
       30.61        32.52        90.28        30.97        26.83        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV 
       29.56        73.81       108.76        12.26         0.30        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G 
       23.93         9.30        23.05        22.78        35.67       114.35 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       11.41        75.65        76.41        55.40        12.53        12.00 
TCGA-DD-AACG TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       15.42        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW 
       61.68        14.20        59.31        51.35        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       44.22        22.09        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADM 
       39.52         3.78        37.64        35.67        35.05         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       29.52        14.89        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       19.30        18.25        18.15        18.61        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.17        21.83        18.90        15.72        25.08        16.37 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        79.07        89.69        82.62 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       76.18        56.48        62.47        66.25        65.39        49.48 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
       13.41        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       12.82        14.04        13.15        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R3 
        0.62         9.96        14.40        23.97         8.12        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33         0.39        13.68        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-A5SM TCGA-G3-A7M6 
       19.53        19.23        25.25        22.95        17.10        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        5.98         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF 
        8.75         3.02         1.02         2.20         2.99        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83         3.72         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G 
       24.36        12.72        13.97        12.03         9.57        18.38 
TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         0.62        10.85        58.88        19.92        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       21.01         3.09        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
       15.52        24.13        17.59        16.44         1.71         7.04 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
       10.32        11.34         0.99        12.99        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           120.82            114.35 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             19.1              19.3 
[1] "0.1 - 120.8 (19.1)" "0.0 - 114.3 (19.3)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED        36       22         0         19          2          4
  6Q LOSS WILD-TYPE     132       62         3         40          6          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q LOSS MUTATED          1         0         1
  6Q LOSS WILD-TYPE        2         1         1
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 36               132
  STAGE II                22                62
  STAGE III                0                 3
  STAGE IIIA              19                40
  STAGE IIIB               2                 6
  STAGE IIIC               4                 3
  STAGE IV                 1                 2
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6Q LOSS MUTATED      40  25  21   3
  6Q LOSS WILD-TYPE   139  66  52   9
D53V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1              40               139
  T2                 25                66
  T3                 21                52
  T4                  3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    64   2
  6Q LOSS WILD-TYPE 185   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     64    2
  6Q LOSS WILD-TYPE  185    1
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              64               185
  1               2                 1
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    71   2
  6Q LOSS WILD-TYPE 189   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     71    2
  6Q LOSS WILD-TYPE  189    2
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              71               189
  1               2                 2
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    38  52
  6Q LOSS WILD-TYPE  75 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     38   52
  6Q LOSS WILD-TYPE   75  192
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              38                75
  MALE                52               192
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6Q LOSS MUTATED                         0                       87
  6Q LOSS WILD-TYPE                       2                      261
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6Q LOSS MUTATED                                  3
  6Q LOSS WILD-TYPE                                4
D53V8, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      87               261
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    80   4   0   5
  6Q LOSS WILD-TYPE 235  11   1  14
D53V9, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              80               235
  R1               4                11
  R2               0                 1
  RX               5                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0    36
  6Q LOSS WILD-TYPE                                1   120
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           3    48
  6Q LOSS WILD-TYPE                        14   125
D53V10, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         36               120
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         48               125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     2  83
  6Q LOSS WILD-TYPE   9 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   83
  6Q LOSS WILD-TYPE    9  246
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              83               246
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     8   5
  7P LOSS WILD-TYPE 217 104
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13               321 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5               104 
$`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         3.19         0.10        12.95        55.69 
TCGA-DD-AACB TCGA-DD-AADB TCGA-DD-AADN TCGA-EP-A2KB TCGA-FV-A3I1 TCGA-K7-A5RG 
       76.41        40.83        29.52        19.59         8.12        17.06 
TCGA-RC-A7SK 
       15.52 

$`7P LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
        0.66        11.97        11.08         1.51        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       37.32        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
        0.26        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 
       13.45        36.66         0.66         0.07         2.86         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-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-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y 
       33.04        18.35        13.64        21.14        27.19         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        90.28        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       11.41        75.65        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.08        40.54        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       18.21        18.87        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       20.98        18.61        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       23.74        18.90        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        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         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        20.61         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         6.38        12.03         0.03         0.33        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39        13.68        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        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80         9.70         9.17         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83         3.72         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85        20.71         0.62        10.85        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        24.13         0.76        17.59        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
        1.71        15.98         7.04        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        0.99        12.99        24.85        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.10              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            76.41            120.82 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            17.06             19.30 
[1] "0.1 - 76.4 (17.1)"  "0.0 - 120.8 (19.3)"
[1] "hr=" "1.4"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P LOSS MUTATED         8        5         0          2          0          0
  7P LOSS WILD-TYPE     160       79         3         57          8          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P LOSS MUTATED          0         0         0
  7P LOSS WILD-TYPE        3         1         2
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  8               160
  STAGE II                 5                79
  STAGE III                0                 3
  STAGE IIIA               2                57
  STAGE IIIB               0                 8
  STAGE IIIC               0                 7
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7P LOSS MUTATED       8   5   2   0
  7P LOSS WILD-TYPE   171  86  71  12
D54V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               8               171
  T2                  5                86
  T3                  2                71
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V5, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    10   0
  7P LOSS WILD-TYPE 239   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     10    0
  7P LOSS WILD-TYPE  239    3
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              10               239
  1               0                 3
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    11   0
  7P LOSS WILD-TYPE 249   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     11    0
  7P LOSS WILD-TYPE  249    4
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              11               249
  1               0                 4
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     7   8
  7P LOSS WILD-TYPE 106 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7    8
  7P LOSS WILD-TYPE  106  236
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               7               106
  MALE                 8               236
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7P LOSS MUTATED                         0                       15
  7P LOSS WILD-TYPE                       2                      333
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7P LOSS MUTATED                                  0
  7P LOSS WILD-TYPE                                7
D54V8, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      15               333
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of 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    14   0   0   1
  7P LOSS WILD-TYPE 301  15   1  18
D54V9, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              14               301
  R1               0                15
  R2               0                 1
  RX               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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     8
  7P LOSS WILD-TYPE                                1   148
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           1     6
  7P LOSS WILD-TYPE                        16   167
D54V10, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8               148
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                          6               167
[1] 4 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
  7P LOSS MUTATED     0  14
  7P LOSS WILD-TYPE  11 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   14
  7P LOSS WILD-TYPE   11  315
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              14               315
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     7  10
  7Q LOSS WILD-TYPE 218  99
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               317 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10                99 
$`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         3.19        12.95        13.64 
TCGA-DD-A39X TCGA-DD-AACB TCGA-DD-AACZ TCGA-DD-AADB TCGA-DD-AADF TCGA-ED-A7PX 
       55.69        76.41         5.62        40.83         3.78         0.20 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-G3-A25S TCGA-K7-A5RG TCGA-QA-A7B7 
        1.84        19.59        13.68        17.06         3.09 

$`7Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        11.97        11.08         1.51        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF 
       23.34         1.12        69.57         5.03        44.42         0.26 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       17.98        14.60        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
       36.66         0.66         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-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z 
       33.04        18.35        21.14        27.19         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       90.28        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       75.65        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI 
       40.54        13.97        40.47        39.52        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV 
       15.06        14.33        66.67        15.58        18.21        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
       19.99         4.64        21.17        21.83        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         9.73        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41        13.35         0.20        18.74        19.99        20.61 
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        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33        81.73         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        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14         3.02         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.91        20.75        16.83         3.72         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        19.92        17.69        21.01        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.04        15.39        15.52        24.13         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       19.76        16.44         1.71        15.98         7.04        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
       10.32        11.34         0.99        12.99        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        40.80        79.30        11.21 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.20              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            76.41            120.82 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            13.68             19.53 
[1] "0.2 - 76.4 (13.7)"  "0.0 - 120.8 (19.5)"
[1] "hr=" "2.5"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q LOSS MUTATED         9        7         0          4          0          0
  7Q LOSS WILD-TYPE     159       77         3         55          8          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q LOSS MUTATED          0         0         0
  7Q LOSS WILD-TYPE        3         1         2
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  9               159
  STAGE II                 7                77
  STAGE III                0                 3
  STAGE IIIA               4                55
  STAGE IIIB               0                 8
  STAGE IIIC               0                 7
  STAGE IV                 0                 3
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7Q LOSS MUTATED       9   7   4   0
  7Q LOSS WILD-TYPE   170  84  69  12
D55V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               9               170
  T2                  7                84
  T3                  4                69
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V5, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    14   0
  7Q LOSS WILD-TYPE 235   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     14    0
  7Q LOSS WILD-TYPE  235    3
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              14               235
  1               0                 3
[1] 2 2
[1] FALSE
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    17   0
  7Q LOSS WILD-TYPE 243   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     17    0
  7Q LOSS WILD-TYPE  243    4
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              17               243
  1               0                 4
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    11   9
  7Q LOSS WILD-TYPE 102 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11    9
  7Q LOSS WILD-TYPE  102  235
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              11               102
  MALE                 9               235
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7Q LOSS MUTATED                         0                       20
  7Q LOSS WILD-TYPE                       2                      328
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7Q LOSS MUTATED                                  0
  7Q LOSS WILD-TYPE                                7
D55V8, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      20               328
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of 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    16   2   0   2
  7Q LOSS WILD-TYPE 299  13   1  17
D55V9, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              16               299
  R1               2                13
  R2               0                 1
  RX               2                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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    10
  7Q LOSS WILD-TYPE                                1   146
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           3     7
  7Q LOSS WILD-TYPE                        14   166
D55V10, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10               146
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                          7               166
[1] 4 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
  7Q LOSS MUTATED     0  19
  7Q LOSS WILD-TYPE  11 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   19
  7Q LOSS WILD-TYPE   11  310
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              19               310
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   118  54
  8P LOSS WILD-TYPE 107  55
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              172               162 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               54                55 
$`8P LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       23.80        63.75        80.28        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        11.74        37.25         1.18         8.55        13.02 
TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       11.97         1.51        37.32        10.13        27.52        27.52 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        5.03        44.42        13.84         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 TCGA-DD-A113 
       12.72        13.45         0.66         3.19         3.39        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A1EE TCGA-DD-A1EG 
       83.57        53.33       113.00        21.76        11.47        45.11 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       33.04        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       25.81        17.59        13.78         0.36        30.61        33.14 
TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NR 
       90.28        30.15        26.83        30.51        39.78         0.30 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACG 
       35.67       114.35        76.41        55.40        63.48        15.42 
TCGA-DD-AACH TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        6.41        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 
       59.31        51.52        47.67         4.50        42.58        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK 
       40.54        40.83        13.97        37.64        35.67        34.49 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADV 
        0.39        29.52        14.89        15.06        14.33        18.87 
TCGA-DD-AAE0 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.25        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.72        25.08        16.37        25.78        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       82.62        59.93        72.39        64.77        62.47        66.25 
TCGA-DD-AAW3 TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A12J 
       53.69        12.82         0.20        14.04         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        20.61         0.62        11.93        22.85        14.40 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 
       23.97        19.10        27.88         8.12         6.38         0.03 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CJ 
       81.73        13.68        28.27        30.74        22.13        19.53 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 
        7.76        12.03         1.84         8.55         9.70         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-LG-A9QC 
        8.75         2.14         3.02         2.99        16.83        13.97 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        9.57        16.67        20.71        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        3.09        21.04        19.04        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
        0.76        19.76         1.71        15.98         7.04        10.75 
TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       11.34        13.55        35.77        23.21        23.57        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        40.80        79.30        11.21 

$`8P LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        83.24        41.79        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
       40.41        20.81        14.99         8.61        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10W 
        0.66        11.08        48.99        27.91        46.78         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BC-A8YO 
       25.32        23.34         1.12        69.57        17.98        18.48 
TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT 
       44.81        36.66         0.07         2.86         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 
        0.10         0.07         0.10         0.13        37.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       19.79        75.65        12.95        49.15         6.02        18.35 
TCGA-DD-A39W TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       27.19         7.66        70.06        20.12       102.74       107.11 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       32.52        30.97        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       12.26        80.75        13.48         0.53        11.41        75.65 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.53        12.00        53.19        69.11         0.30         3.52 
TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD1 
       51.35        50.33        46.82         5.59         5.62        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       21.63        44.22        22.09        40.47        39.52         3.78 
TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       35.05        20.91        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAEA TCGA-DD-AAEG 
       18.25        18.15        20.98        18.61        18.90        23.64 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-DD-AAW2 
       50.33        35.08        76.18        56.48        65.39        49.48 
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         9.73 
TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB 
        0.20        13.15        13.41        13.35         0.20        19.59 
TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T 
        9.96        60.89        12.03         0.33         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M7 
       19.23        25.25        22.95        20.42        17.10         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 
       11.24        11.80         9.17         1.02         2.20        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        17.06         3.72         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75G TCGA-MI-A75H TCGA-MR-A520 
       24.36        12.72        12.03        18.38        12.85         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-RC-A7SB TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0V 
       10.85        58.88        19.33        17.59        16.44        10.32 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CY TCGA-ZP-A9D1 TCGA-ZS-A9CD 
        0.99        12.99        24.85        25.71         0.69        45.57 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.03              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           114.35            120.82 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           19.955            18.510 
[1] "0.0 - 114.3 (20.0)" "0.1 - 120.8 (18.5)"
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P LOSS MUTATED        87       45         0         26          7          4
  8P LOSS WILD-TYPE      81       39         3         33          1          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P LOSS MUTATED          2         1         1
  8P LOSS WILD-TYPE        1         0         1
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 87                81
  STAGE II                45                39
  STAGE III                0                 3
  STAGE IIIA              26                33
  STAGE IIIB               7                 1
  STAGE IIIC               4                 3
  STAGE IV                 2                 1
  STAGE IVA                1                 0
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  8P LOSS MUTATED      94 52 34  5
  8P LOSS WILD-TYPE    85 39 39  7
D56V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              94                85
  T2                 52                39
  T3                 34                39
  T4                  5                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   121   3
  8P LOSS WILD-TYPE 128   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    121    3
  8P LOSS WILD-TYPE  128    0
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             121               128
  1               3                 0
[1] 2 2
[1] FALSE
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   130   2
  8P LOSS WILD-TYPE 130   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    130    2
  8P LOSS WILD-TYPE  130    2
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             130               130
  1               2                 2
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    59 126
  8P LOSS WILD-TYPE  54 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     59  126
  8P LOSS WILD-TYPE   54  118
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              59                54
  MALE               126               118
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8P LOSS MUTATED                         0                      184
  8P LOSS WILD-TYPE                       2                      164
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8P LOSS MUTATED                                  1
  8P LOSS WILD-TYPE                                6
D56V8, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     184               164
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   163   9   0   9
  8P LOSS WILD-TYPE 152   6   1  10
D56V9, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             163               152
  R1               9                 6
  R2               0                 1
  RX               9                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
  8P LOSS MUTATED                                  1    76
  8P LOSS WILD-TYPE                                0    80
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          13    90
  8P LOSS WILD-TYPE                         4    83
D56V10, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         76                80
  BLACK OR AFRICAN AMERICAN                     13                 4
  WHITE                                         90                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"
D56V11, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     7 170
  8P LOSS WILD-TYPE   4 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      7  170
  8P LOSS WILD-TYPE    4  159
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                 4
  NOT HISPANIC OR LATINO             170               159
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    27  12
  8Q LOSS WILD-TYPE 198  97
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               39               295 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12                97 
$`8Q LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GX TCGA-5R-AAAM TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KG 
       23.80        80.28         1.51        27.52        13.84        22.36 
TCGA-BW-A5NO TCGA-CC-5261 TCGA-DD-A115 TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4NA 
        0.66         3.19        83.57        25.81        30.61        33.14 
TCGA-DD-A4NK TCGA-DD-A73C TCGA-DD-AACE TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD8 
       39.78        23.05        63.48        47.67         4.50        40.08 
TCGA-DD-AADP TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE6 TCGA-DD-AAEB TCGA-DD-AAVU 
       15.06        18.87        19.30         4.64        15.72        72.39 
TCGA-ED-A7PY TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25V TCGA-G3-A7M9 TCGA-G3-AAV2 
       12.82        27.88         0.03        28.27         1.84         9.70 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-T1-A6J8 
        0.89         2.14        19.92         3.09        21.04         0.76 
TCGA-UB-A7MF TCGA-WJ-A86L TCGA-ZS-A9CF 
        7.04        11.34        79.30 

$`8Q LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        41.33        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        37.25        20.81        14.99         1.18         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
       13.02         8.61        10.78        10.59         0.66        11.97 
TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       11.08        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
        5.03        44.42         0.26        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 
       18.48        44.81        13.45        36.66         0.07         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        79.73        37.78        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        11.47        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        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        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        90.28        30.97        30.15        26.83        30.51 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        23.93         9.30        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       76.41        55.40        12.53        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 
       50.33        46.82         5.59         5.62        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       42.58        44.22        22.09        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ 
       34.49        20.91         0.39        29.52        14.89        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       66.67        15.58        18.21        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       20.98        18.61        19.99        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       18.90        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       35.08        79.07        89.69        82.62        59.93        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        9.73         0.20         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.59         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       60.89        23.97        19.10         8.12         6.38        12.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        81.73         0.39        13.68        51.06        53.79 
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        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       17.10         7.76        12.03         5.98        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.80         9.17         8.75         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        11.84        13.38        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7SB 
        0.62        10.85        58.88        17.69        21.01        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        24.13        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        10.32         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       12.99        24.85        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        40.80 
TCGA-ZS-A9CG 
       11.21 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.03              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            83.57            120.82 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            19.30             19.23 
[1] "0.0 - 83.6 (19.3)"  "0.1 - 120.8 (19.2)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q LOSS MUTATED        17       10         0          9          1          1
  8Q LOSS WILD-TYPE     151       74         3         50          7          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q LOSS MUTATED          1         0         1
  8Q LOSS WILD-TYPE        2         1         1
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 17               151
  STAGE II                10                74
  STAGE III                0                 3
  STAGE IIIA               9                50
  STAGE IIIB               1                 7
  STAGE IIIC               1                 6
  STAGE IV                 1                 2
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8Q LOSS MUTATED      18  12  10   2
  8Q LOSS WILD-TYPE   161  79  63  10
D57V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1              18               161
  T2                 12                79
  T3                 10                63
  T4                  2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    25   1
  8Q LOSS WILD-TYPE 224   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     25    1
  8Q LOSS WILD-TYPE  224    2
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              25               224
  1               1                 2
[1] 2 2
[1] FALSE
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    31   1
  8Q LOSS WILD-TYPE 229   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     31    1
  8Q LOSS WILD-TYPE  229    3
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              31               229
  1               1                 3
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    19  23
  8Q LOSS WILD-TYPE  94 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     19   23
  8Q LOSS WILD-TYPE   94  221
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              19                94
  MALE                23               221
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8Q LOSS MUTATED                         0                       41
  8Q LOSS WILD-TYPE                       2                      307
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8Q LOSS MUTATED                                  1
  8Q LOSS WILD-TYPE                                6
D57V8, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      41               307
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    36   2   0   4
  8Q LOSS WILD-TYPE 279  13   1  15
D57V9, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              36               279
  R1               2                13
  R2               0                 1
  RX               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0    16
  8Q LOSS WILD-TYPE                                1   140
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           2    24
  8Q LOSS WILD-TYPE                        15   149
D57V10, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         16               140
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         24               149
[1] 4 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
  8Q LOSS MUTATED     1  39
  8Q LOSS WILD-TYPE  10 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   39
  8Q LOSS WILD-TYPE   10  290
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              39               290
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    68  35
  9P LOSS WILD-TYPE 157  74
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              103               231 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               35                74 
$`9P LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 
       23.80        63.75        24.89        56.91        41.33        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 
       11.74        20.81        13.02        10.78        10.59        48.99 
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-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
       17.98        14.60         0.07         4.24         3.32         0.10 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        0.10         0.13        79.73        83.57        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-A3A0 TCGA-DD-A3A9 
       33.04        18.35        55.69         5.62        25.81        30.61 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-AA3A TCGA-DD-AACE TCGA-DD-AACG 
       90.28        26.83        73.81        13.48        63.48        15.42 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD3 
       61.68        13.64        51.52        46.82         5.62        42.58 
TCGA-DD-AADC TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADV 
       13.97        34.49        20.91        14.89        15.06        18.87 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE 
       18.15        18.61         4.64        21.83        25.08        16.37 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 
       35.08        89.69        72.39        76.18        62.47        66.25 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A2KC 
       13.41        13.35         0.20        13.15         0.20         0.62 
TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-AAV1 
       11.93        23.97         8.12        13.68        51.06        11.80 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K8 TCGA-MI-A75G TCGA-MI-A75I 
        2.14         3.02         2.20        24.36        18.38        20.71 
TCGA-NI-A8LF TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       19.92        19.33        19.04        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D0 
        0.76        15.98        10.75         0.99        12.99        23.57 
TCGA-ZP-A9D2 
       24.43 

$`9P LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        83.24        41.79        80.28        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       40.41        47.74        37.25        14.99         1.18         8.55 
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
        8.61         0.66        11.97        11.08         1.51        27.91 
TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       44.42         0.26        22.36        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45        36.66         0.66         2.86         3.19         3.39 
TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        0.07        37.78       113.00        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EL 
       66.31        19.79        75.65        11.47        49.15        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        27.19        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-A4NA 
       20.12       102.74       107.11        13.78         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      114.35         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.53        12.00         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
        3.52        58.16        42.81        14.20        59.31        51.35 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       50.33         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD 
       44.22        22.09        40.08        40.54        40.83        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADM 
       39.52         3.78        37.64        35.67        35.05         0.39 
TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       29.52        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 
       18.25        18.25        20.98        19.99        21.17        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       18.90        15.72        23.64        25.78        50.33        79.07 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 
       82.62        59.93        56.48        64.77        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       53.69        12.69        15.85        13.91         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J 
       12.82        14.04        13.41        13.35         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        20.61        19.59         9.96        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        19.10        27.88         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33        81.73         0.39        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        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        9.70         9.17         0.89         8.75         1.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.91        20.75        17.06        16.83         3.72         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.84        13.38        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       16.67        12.85         0.62        10.85        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       21.01         3.09        21.04        17.59        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-YA-A8S7 
        1.71         7.04        10.32        11.34        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       35.77        25.71        23.21         0.69        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            90.28            120.82 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            18.25             19.79 
[1] "0.1 - 90.3 (18.2)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P LOSS MUTATED        49       27         0         20          2          2
  9P LOSS WILD-TYPE     119       57         3         39          6          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P LOSS MUTATED          2         1         2
  9P LOSS WILD-TYPE        1         0         0
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 49               119
  STAGE II                27                57
  STAGE III                0                 3
  STAGE IIIA              20                39
  STAGE IIIB               2                 6
  STAGE IIIC               2                 5
  STAGE IV                 2                 1
  STAGE IVA                1                 0
  STAGE IVB                2                 0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9P LOSS MUTATED      54  31  26   4
  9P LOSS WILD-TYPE   125  60  47   8
D58V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              54               125
  T2                 31                60
  T3                 26                47
  T4                  4                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    80   2
  9P LOSS WILD-TYPE 169   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     80    2
  9P LOSS WILD-TYPE  169    1
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              80               169
  1               2                 1
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    84   3
  9P LOSS WILD-TYPE 176   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     84    3
  9P LOSS WILD-TYPE  176    1
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              84               176
  1               3                 1
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    29  86
  9P LOSS WILD-TYPE  84 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     29   86
  9P LOSS WILD-TYPE   84  158
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              29                84
  MALE                86               158
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9P LOSS MUTATED                         0                      113
  9P LOSS WILD-TYPE                       2                      235
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9P LOSS MUTATED                                  2
  9P LOSS WILD-TYPE                                5
D58V8, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     113               235
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    99   6   1   7
  9P LOSS WILD-TYPE 216   9   0  12
D58V9, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              99               216
  R1               6                 9
  R2               1                 0
  RX               7                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
  9P LOSS MUTATED                                  0    59
  9P LOSS WILD-TYPE                                1    97
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           6    49
  9P LOSS WILD-TYPE                        11   124
D58V10, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         59                97
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         49               124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2 110
  9P LOSS WILD-TYPE   9 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2  110
  9P LOSS WILD-TYPE    9  219
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO             110               219
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    64  34
  9Q LOSS WILD-TYPE 161  75
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               98               236 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               34                75 
$`9Q LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       23.80        63.75        56.91        41.33        18.25        11.74 
TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q 
       20.81         1.18        13.02        10.78        10.59        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 
       10.13        46.78        27.52         5.03        13.84        17.98 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
       14.60         0.07         2.86         4.24         3.32         0.10 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        0.10         0.13        79.73        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ 
        0.46        21.76        12.95        45.11         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NI 
       18.35        55.69         5.62        30.61        33.14        26.83 
TCGA-DD-A4NO TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AACP 
       73.81        13.48        76.41        63.48        61.68        13.64 
TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADK TCGA-DD-AADL 
       51.52         5.62        42.58        40.08        34.49        20.91 
TCGA-DD-AADO TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK 
       14.89        18.87        21.83        18.90        25.08        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 
       89.69        72.39        76.18        62.47        66.25        13.41 
TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ 
       13.35         0.20        13.15         0.62        11.93        23.97 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T 
       27.88         8.12         6.38        12.03        13.68        51.06 
TCGA-G3-A3CH TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-MI-A75G 
       25.64        11.80         2.14         3.02         2.20        18.38 
TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       20.71        19.92        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-AB4B 
       24.13         0.76        15.98         7.04        10.75        12.99 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       23.57        24.43 

$`9Q LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        83.24        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HB 
      120.82        40.41        47.74        37.25        14.99         8.55 
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.61         0.66        11.97        11.08         1.51        48.99 
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-BC-A8YO 
       69.57        44.42         0.26        22.36        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 
       44.81        13.45        36.66         0.66         3.19         3.39 
TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 
        0.07        37.78        83.57       113.00        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.40        66.31        19.79        75.65        11.47        49.15 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14        27.19        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
        0.36        32.52        90.28        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        35.67       114.35         0.53        11.41        75.65 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ 
       69.11         0.30         3.52        58.16        42.81        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       59.31        51.35        50.33        46.82         5.59        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
        4.50        18.54        21.63        44.22        22.09        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       35.67        35.05         0.39        29.52        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.15        20.98        18.61        19.99         4.64        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        16.37        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 
       79.07        82.62        59.93        56.48        64.77        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       49.48        53.69        12.69        15.85        13.91         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        12.82        14.04        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        20.61        19.59         9.96 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A495 TCGA-FV-A496 
       22.85        14.40        60.89        19.10         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       81.73         0.39        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        22.13         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
        5.98         1.84        11.24         8.55         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        0.89         8.75         1.02         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83         3.72         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       12.85         0.62        10.85        58.88        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
        3.09        21.04        17.59        19.76        16.44         1.71 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       10.32        11.34         0.99        24.85        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       25.71        23.21         0.69        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            89.69            120.82 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           18.300            19.775 
[1] "0.1 - 89.7 (18.3)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED        44       25         0         16          2          4
  9Q LOSS WILD-TYPE     124       59         3         43          6          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q LOSS MUTATED          2         1         2
  9Q LOSS WILD-TYPE        1         0         0
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 44               124
  STAGE II                25                59
  STAGE III                0                 3
  STAGE IIIA              16                43
  STAGE IIIB               2                 6
  STAGE IIIC               4                 3
  STAGE IV                 2                 1
  STAGE IVA                1                 0
  STAGE IVB                2                 0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9Q LOSS MUTATED      49  30  21   5
  9Q LOSS WILD-TYPE   130  61  52   7
D59V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1              49               130
  T2                 30                61
  T3                 21                52
  T4                  5                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    67   3
  9Q LOSS WILD-TYPE 182   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     67    3
  9Q LOSS WILD-TYPE  182    0
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              67               182
  1               3                 0
[1] 2 2
[1] FALSE
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    71   3
  9Q LOSS WILD-TYPE 189   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     71    3
  9Q LOSS WILD-TYPE  189    1
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              71               189
  1               3                 1
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    28  77
  9Q LOSS WILD-TYPE  85 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     28   77
  9Q LOSS WILD-TYPE   85  167
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              28                85
  MALE                77               167
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9Q LOSS MUTATED                         0                      103
  9Q LOSS WILD-TYPE                       2                      245
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9Q LOSS MUTATED                                  2
  9Q LOSS WILD-TYPE                                5
D59V8, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     103               245
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    89   5   1   8
  9Q LOSS WILD-TYPE 226  10   0  11
D59V9, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              89               226
  R1               5                10
  R2               1                 0
  RX               8                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 LOSS MUTATED                                  0    50
  9Q LOSS WILD-TYPE                                1   106
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           6    49
  9Q LOSS WILD-TYPE                        11   124
D59V10, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         50               106
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         49               124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2 102
  9Q LOSS WILD-TYPE   9 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2  102
  9Q LOSS WILD-TYPE    9  227
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO             102               227
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    33   8
  10P LOSS WILD-TYPE 192 101
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                41                293 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                101 
$`10P LOSS MUTATED`
TCGA-2Y-A9H2 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A2L6 
       56.91         5.03        13.84        17.98        18.48        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A11C 
       13.45         0.66         0.10         0.07         0.13        21.76 
TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NQ TCGA-DD-AACG TCGA-DD-AACO TCGA-DD-AACU 
        5.62        26.83        12.26        15.42        61.68        51.52 
TCGA-DD-AACV TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADR TCGA-DD-AAVU TCGA-ED-A7PX 
       50.33        40.08        40.54        66.67        72.39         0.20 
TCGA-ED-A7XO TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A25X TCGA-G3-AAV1 
       14.04         0.20        23.97        27.88        58.49        11.80 
TCGA-G3-AAV4 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-NI-A4U2 TCGA-QA-A7B7 
        0.89        17.06        11.84        13.38        58.88         3.09 
TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       24.13         0.99         0.69        40.80        79.30 

$`10P LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       24.89        27.88       120.82        40.41        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        8.55        13.02         8.61        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       11.97        11.08         1.51        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.34         1.12        69.57        44.42         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       14.60        12.72        36.66         0.07         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 
        3.39         4.24         3.32         0.10        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       18.35        13.64        21.14        27.19        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       90.28        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        73.81       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        63.48        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP 
       69.11         0.30         3.52        58.16        42.81        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       14.20        59.31        51.35        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       22.09        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
       29.52        14.89        15.06        14.33        15.58        18.21 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.87        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       18.90        15.72        25.08        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        79.07        89.69        82.62        59.93 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         9.73        12.82         0.20        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.35         1.84        18.74        19.99        20.61        19.59 
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        60.89 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10         8.12         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       81.73         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.70         9.17         8.75         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.91        20.75        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       19.92        17.69        21.01        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52         0.76        17.59        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
        1.71        15.98         7.04        10.75        10.32        11.34 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       12.99        24.85        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.57        24.43        12.99        45.57        11.21 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             79.30             120.82 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             17.06              19.53 
[1] "0.1 - 79.3 (17.1)"  "0.0 - 120.8 (19.5)"
[1] "hr=" "1.5"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10P LOSS MUTATED        15       13         0          9          0
  10P LOSS WILD-TYPE     153       71         3         50          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P LOSS MUTATED            2        0         1         0
  10P LOSS WILD-TYPE          5        3         0         2
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  15                153
  STAGE II                 13                 71
  STAGE III                 0                  3
  STAGE IIIA                9                 50
  STAGE IIIB                0                  8
  STAGE IIIC                2                  5
  STAGE IV                  0                  3
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10P LOSS MUTATED      17  14  11   2
  10P LOSS WILD-TYPE   162  77  62  10
D60V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1               17                162
  T2                  14                 77
  T3                  11                 62
  T4                   2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    25   1
  10P LOSS WILD-TYPE 224   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     25    1
  10P LOSS WILD-TYPE  224    2
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               25                224
  1                1                  2
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    31   0
  10P LOSS WILD-TYPE 229   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     31    0
  10P LOSS WILD-TYPE  229    4
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               31                229
  1                0                  4
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    13  31
  10P LOSS WILD-TYPE 100 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     13   31
  10P LOSS WILD-TYPE  100  213
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               13                100
  MALE                 31                213
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10P LOSS MUTATED                         0                       41
  10P LOSS WILD-TYPE                       2                      307
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10P LOSS MUTATED                                  3
  10P LOSS WILD-TYPE                                4
D60V8, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       41                307
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    39   1   0   4
  10P LOSS WILD-TYPE 276  14   1  15
D60V9, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               39                276
  R1                1                 14
  R2                0                  1
  RX                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0    19
  10P LOSS WILD-TYPE                                1   137
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           5    20
  10P LOSS WILD-TYPE                        12   153
D60V10, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          19                137
  BLACK OR AFRICAN AMERICAN                       5                 12
  WHITE                                          20                153
[1] 4 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
  10P LOSS MUTATED     1  39
  10P LOSS WILD-TYPE  10 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   39
  10P LOSS WILD-TYPE   10  290
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               39                290
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    46  21
  10Q LOSS WILD-TYPE 179  88
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                67                267 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                21                 88 
$`10Q LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R 
       23.80        56.91        47.74         0.66        37.32        10.13 
TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A2L6 
        2.99         5.03        13.84        17.98        18.48        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
       13.45         0.66         2.86         3.32         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EL 
        0.13        37.78         2.60        21.76        45.11        13.64 
TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NQ TCGA-DD-AACG TCGA-DD-AACO TCGA-DD-AACQ 
        5.62        26.83        12.26        15.42        61.68        14.20 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
       51.52        50.33         5.62        42.58        44.22        40.08 
TCGA-DD-AADA TCGA-DD-AADL TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE8 TCGA-ED-A459 
       40.54        20.91        66.67        18.25        21.83        13.41 
TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A3I0 
        0.20        14.04         1.84         0.20        23.97        27.88 
TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A5SJ TCGA-G3-AAV1 TCGA-G3-AAV4 
        0.33        53.79        58.49        22.95        11.80         0.89 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-QA-A7B7 
       17.06        11.84        13.38        10.85        58.88         3.09 
TCGA-RC-A7SB TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MD TCGA-WQ-A9G7 TCGA-ZP-A9D1 
       19.33        15.52        24.13         1.71         0.99         0.69 
TCGA-ZS-A9CE 
       40.80 

$`10Q LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       27.88       120.82        40.41        41.33        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       37.25        20.81        14.99         1.18         8.55        13.02 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
        8.61        10.78        10.59        11.97        11.08         1.51 
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-A3KG 
       23.34         1.12        69.57        44.42         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72        36.66         0.07         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        4.24         0.10        79.73        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         0.46        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        11.47        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       33.04        18.35        21.14        27.19        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       90.28        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        73.81       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        63.48        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP 
       69.11         0.30         3.52        58.16        42.81        13.64 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       59.31        51.35        46.82         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       18.54        21.63        22.09        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
        0.39        29.52        14.89        15.06        14.33        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        18.87        19.30        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA 
       18.61        19.99         4.64        21.17        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        53.69        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        9.73        12.82         0.20        13.15        13.41        13.35 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         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        60.89        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38        12.03         0.03        81.73         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       51.06        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL 
       25.64         5.92        19.53        19.23        25.25        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
        8.55         9.70         9.17         8.75         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
        1.02         2.20         2.99        37.91        20.75        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
        3.72         2.14        24.36        12.72        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
        9.57        16.67        18.38        12.85        20.71         0.62 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
       19.92        17.69        21.01        21.04        19.04        15.39 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
        0.76        17.59        19.76        16.44        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
       10.75        10.32        11.34        12.99        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             66.67             120.82 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             15.42              19.79 
[1] "0.1 - 66.7 (15.4)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED        30       17         0         14          1
  10Q LOSS WILD-TYPE     138       67         3         45          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q LOSS MUTATED            3        1         1         0
  10Q LOSS WILD-TYPE          4        2         0         2
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  30                138
  STAGE II                 17                 67
  STAGE III                 0                  3
  STAGE IIIA               14                 45
  STAGE IIIB                1                  7
  STAGE IIIC                3                  4
  STAGE IV                  1                  2
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10Q LOSS MUTATED      32  20  17   5
  10Q LOSS WILD-TYPE   147  71  56   7
D61V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1               32                147
  T2                  20                 71
  T3                  17                 56
  T4                   5                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    49   1
  10Q LOSS WILD-TYPE 200   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     49    1
  10Q LOSS WILD-TYPE  200    2
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               49                200
  1                1                  2
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    55   0
  10Q LOSS WILD-TYPE 205   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     55    0
  10Q LOSS WILD-TYPE  205    4
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               55                205
  1                0                  4
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    21  53
  10Q LOSS WILD-TYPE  92 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     21   53
  10Q LOSS WILD-TYPE   92  191
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               21                 92
  MALE                 53                191
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10Q LOSS MUTATED                         1                       69
  10Q LOSS WILD-TYPE                       1                      279
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10Q LOSS MUTATED                                  4
  10Q LOSS WILD-TYPE                                3
D61V8, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       69                279
  HEPATOCHOLANGIOCARCINOMA (MIXED)                4                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    63   3   0   7
  10Q LOSS WILD-TYPE 252  12   1  12
D61V9, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               63                252
  R1                3                 12
  R2                0                  1
  RX                7                 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 LOSS MUTATED                                  0    38
  10Q LOSS WILD-TYPE                                1   118
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          10    26
  10Q LOSS WILD-TYPE                         7   147
D61V10, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          38                118
  BLACK OR AFRICAN AMERICAN                      10                  7
  WHITE                                          26                147
[1] 4 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
  10Q LOSS MUTATED     2  67
  10Q LOSS WILD-TYPE   9 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   67
  10Q LOSS WILD-TYPE    9  262
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               67                262
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    37  18
  11P LOSS WILD-TYPE 188  91
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                55                279 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                 91 
$`11P LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-2Y-A9H6 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       23.80        24.89        41.33        11.74        13.02        10.78 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 TCGA-BC-A217 
        0.66        11.08        37.32        46.78         5.03        13.84 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A1E9 
        0.10         0.07         0.13        79.73        83.57        90.71 
TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NI 
       12.95        33.04        55.69        32.52        90.28        26.83 
TCGA-DD-AACB TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADD 
       76.41        61.68        13.64        44.22        22.09        40.47 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-ED-A7PZ TCGA-ED-A7XO 
       29.52        14.89        18.61        35.08         0.20        14.04 
TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        1.84         0.62        23.97         0.33        81.73        13.68 
TCGA-G3-A5SJ TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-KR-A7K2 
       22.95         1.84        11.80         2.14         3.02        11.84 
TCGA-KR-A7K7 TCGA-MI-A75G TCGA-RC-A7SB TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
       13.38        18.38        19.33        24.13        17.59        16.44 
TCGA-YA-A8S7 
       13.55 

$`11P LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H7 
      120.82        40.41        56.91        47.74        18.25        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        14.99         1.18         8.55         8.61        10.59 
TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T 
       11.97         1.51        48.99        27.91        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42         0.26        22.36        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       18.48        44.81        13.45        36.66         0.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB 
        2.86         3.19         3.39         4.24         3.32         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 
       11.47        45.11        49.15         6.02        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        27.19         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
        0.36        30.61        33.14        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       11.41        75.65        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       58.16        42.81        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       18.54        21.63        42.58        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       13.97        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       34.49        20.91         0.39        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       15.58        18.21        18.87        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.15        20.98        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       23.74        18.90        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        49.48        53.69        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         9.73         0.20        12.82        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41        13.35         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       19.59         9.96        11.93        22.85        14.40        60.89 
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        12.03         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       19.23        25.25        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        5.98        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        8.75         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06        16.83         3.72         2.14        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        0.62        10.85        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 
        3.09        21.04        19.04        15.39        15.52         0.76 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       19.76         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34         0.99        12.99        24.85        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             90.71             120.82 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             17.59              19.59 
[1] "0.1 - 90.7 (17.6)"  "0.0 - 120.8 (19.6)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P LOSS MUTATED        19       16         0         16          2
  11P LOSS WILD-TYPE     149       68         3         43          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P LOSS MUTATED            2        2         1         0
  11P LOSS WILD-TYPE          5        1         0         2
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  19                149
  STAGE II                 16                 68
  STAGE III                 0                  3
  STAGE IIIA               16                 43
  STAGE IIIB                2                  6
  STAGE IIIC                2                  5
  STAGE IV                  2                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11P LOSS MUTATED      21  19  20   1
  11P LOSS WILD-TYPE   158  72  53  11
D62V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               21                158
  T2                  19                 72
  T3                  20                 53
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    41   2
  11P LOSS WILD-TYPE 208   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     41    2
  11P LOSS WILD-TYPE  208    1
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               41                208
  1                2                  1
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    46   1
  11P LOSS WILD-TYPE 214   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     46    1
  11P LOSS WILD-TYPE  214    3
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               46                214
  1                1                  3
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    18  43
  11P LOSS WILD-TYPE  95 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     18   43
  11P LOSS WILD-TYPE   95  201
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               18                 95
  MALE                 43                201
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11P LOSS MUTATED                         1                       57
  11P LOSS WILD-TYPE                       1                      291
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11P LOSS MUTATED                                  3
  11P LOSS WILD-TYPE                                4
D62V8, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       57                291
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    54   4   0   3
  11P LOSS WILD-TYPE 261  11   1  16
D62V9, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               54                261
  R1                4                 11
  R2                0                  1
  RX                3                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0    25
  11P LOSS WILD-TYPE                                1   131
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           3    33
  11P LOSS WILD-TYPE                        14   140
D62V10, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          25                131
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          33                140
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4  53
  11P LOSS WILD-TYPE   7 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4   53
  11P LOSS WILD-TYPE    7  276
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               53                276
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    43  20
  11Q LOSS WILD-TYPE 182  89
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                63                271 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                20                 89 
$`11Q LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-2Y-A9H6 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       23.80        24.89        41.33        11.74        13.02        10.78 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 
        0.66        11.08        27.91        37.32        46.78         5.03 
TCGA-BC-A217 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 
       13.84         4.24         0.10         0.13        79.73        83.57 
TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB 
        2.60        90.71        12.95        33.04        55.69        32.52 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A73B TCGA-DD-AACB TCGA-DD-AACO TCGA-DD-AACP 
       90.28        26.83         9.30        76.41        61.68        13.64 
TCGA-DD-AACV TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADO 
       50.33        44.22        22.09        40.08        40.47        14.89 
TCGA-DD-AADP TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEK 
       15.06        18.25        18.61         4.64        25.08        35.08 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A496 
        0.20        14.04         1.84         0.62        23.97         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV6 
       81.73        13.68        22.95        11.80         9.70         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA 
       11.84        13.38        19.33        19.04        24.13        17.59 
TCGA-UB-A7MC TCGA-UB-A7MF TCGA-YA-A8S7 
       16.44         7.04        13.55 

$`11Q LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H7 
      120.82        40.41        56.91        47.74        18.25        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        14.99         1.18         8.55         8.61        10.59 
TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       11.97         1.51        48.99        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
        0.26        22.36        17.98        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       44.81        13.45        36.66         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 
        3.19         3.39         3.32         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        11.47        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       49.15         6.02        18.35        13.64        21.14        27.19 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
      114.35        13.48         0.53        11.41        75.65        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ 
       69.11         0.30         3.52        58.16        42.81        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       59.31        51.35        51.52        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA 
        5.62         4.50        18.54        21.63        42.58        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.83        13.97        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ 
       35.05        34.49        20.91         0.39        29.52        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 
       66.67        15.58        18.21        18.87        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.15        20.98        19.99        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       18.90        15.72        16.37        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        9.73         0.20        12.82        13.15        13.41        13.35 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        20.61        19.59         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        60.89        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        12.03         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
       11.24         8.55         9.17         0.89         8.75         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       16.83         3.72         2.14        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        0.62        10.85        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MB 
        3.09        21.04        15.39        15.52         0.76        19.76 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
        1.71        15.98        10.75        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       12.99        24.85        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.10               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             90.71             120.82 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             17.59              19.76 
[1] "0.1 - 90.7 (17.6)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1"  
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11Q LOSS MUTATED        28       14         0         19          1
  11Q LOSS WILD-TYPE     140       70         3         40          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q LOSS MUTATED            2        2         1         0
  11Q LOSS WILD-TYPE          5        1         0         2
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  28                140
  STAGE II                 14                 70
  STAGE III                 0                  3
  STAGE IIIA               19                 40
  STAGE IIIB                1                  7
  STAGE IIIC                2                  5
  STAGE IV                  2                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11Q LOSS MUTATED      30  17  22   1
  11Q LOSS WILD-TYPE   149  74  51  11
D63V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               30                149
  T2                  17                 74
  T3                  22                 51
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    51   2
  11Q LOSS WILD-TYPE 198   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     51    2
  11Q LOSS WILD-TYPE  198    1
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               51                198
  1                2                  1
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    55   1
  11Q LOSS WILD-TYPE 205   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     55    1
  11Q LOSS WILD-TYPE  205    3
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               55                205
  1                1                  3
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    22  48
  11Q LOSS WILD-TYPE  91 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     22   48
  11Q LOSS WILD-TYPE   91  196
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               22                 91
  MALE                 48                196
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11Q LOSS MUTATED                         1                       66
  11Q LOSS WILD-TYPE                       1                      282
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11Q LOSS MUTATED                                  3
  11Q LOSS WILD-TYPE                                4
D63V8, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       66                282
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    61   5   0   4
  11Q LOSS WILD-TYPE 254  10   1  15
D63V9, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               61                254
  R1                5                 10
  R2                0                  1
  RX                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0    31
  11Q LOSS WILD-TYPE                                1   125
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           4    35
  11Q LOSS WILD-TYPE                        13   138
D63V10, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          31                125
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          35                138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     5  61
  11Q LOSS WILD-TYPE   6 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      5   61
  11Q LOSS WILD-TYPE    6  268
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  6
  NOT HISPANIC OR LATINO               61                268
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    37  17
  12P LOSS WILD-TYPE 188  92
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                54                280 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                17                 92 
$`12P LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BD-A2L6 
       23.80         8.55        13.02        13.84        17.98        44.81 
TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ 
        3.32         0.13         7.33        45.11        49.15        33.04 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A4NA TCGA-DD-A4NH 
       13.64        55.69         5.62         7.66        33.14        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A73F TCGA-DD-AACE TCGA-DD-AACG 
       26.83        30.51        73.81        35.67        63.48        15.42 
TCGA-DD-AACN TCGA-DD-AACU TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADM 
       42.81        51.52        47.67        44.22        40.08         0.39 
TCGA-DD-AADO TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       14.89        18.61        16.37        50.33        35.08        79.07 
TCGA-DD-AAVU TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A3R2 
       72.39        13.15         0.20         0.62         8.12         6.38 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Z TCGA-G3-A7M6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        0.33        13.68        21.53        12.03         3.02         1.02 
TCGA-MI-A75G TCGA-MI-A75I TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-AA0U TCGA-ZP-A9D1 
       18.38        20.71        15.52         0.76        10.75         0.69 

$`12P LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.61        10.78        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        1.51        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
       69.57         5.03        44.42         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       12.72        18.48        13.45        36.66         0.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.19         3.39         4.24         0.10         0.07 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI 
       66.31        19.79        75.65        11.47        12.95         6.02 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
       18.35        21.14        27.19        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        90.28        30.97        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G 
       23.93         9.30        23.05        22.78         1.45       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.53        12.00         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        3.52        58.16        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       51.35        50.33        46.82         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB 
       18.54        21.63        42.58        22.09        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       35.05        34.49        20.91        29.52        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       66.67        15.58        18.21        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        18.15        20.98        19.99         4.64        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG 
       21.83        23.74        18.90        15.72        25.08        23.64 
TCGA-DD-AAEH TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       25.78        89.69        82.62        59.93        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
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         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 
        0.20        12.82         0.20        14.04        13.41        13.35 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        1.84        18.74        19.99        20.61        19.59         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
       27.88        12.03         0.03        81.73         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
       53.79        28.27        30.74        58.49        14.86        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       20.42        17.10         7.76         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
        8.55        11.80         9.70         9.17         0.89         8.75 
TCGA-G3-AAV6 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        2.14         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83         3.72         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72        13.97        12.03         9.57        16.67        12.85 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        0.62        10.85        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
        3.09        21.04        19.33        19.04        15.39        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       17.59        19.76        16.44         1.71        15.98         7.04 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
       10.32        11.34         0.99        12.99        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.13               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             79.07             120.82 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            17.175             19.560 
[1] "0.1 - 79.1 (17.2)"  "0.0 - 120.8 (19.6)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED        24       15         1          8          3
  12P LOSS WILD-TYPE     144       69         2         51          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P LOSS MUTATED            2        3         0         0
  12P LOSS WILD-TYPE          5        0         1         2
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  24                144
  STAGE II                 15                 69
  STAGE III                 1                  2
  STAGE IIIA                8                 51
  STAGE IIIB                3                  5
  STAGE IIIC                2                  5
  STAGE IV                  3                  0
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12P LOSS MUTATED      27  20  12   1
  12P LOSS WILD-TYPE   152  71  61  11
D64V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1               27                152
  T2                  20                 71
  T3                  12                 61
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    40   2
  12P LOSS WILD-TYPE 209   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     40    2
  12P LOSS WILD-TYPE  209    1
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               40                209
  1                2                  1
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    46   2
  12P LOSS WILD-TYPE 214   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     46    2
  12P LOSS WILD-TYPE  214    2
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               46                214
  1                2                  2
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    17  43
  12P LOSS WILD-TYPE  96 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     17   43
  12P LOSS WILD-TYPE   96  201
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               17                 96
  MALE                 43                201
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12P LOSS MUTATED                         0                       59
  12P LOSS WILD-TYPE                       2                      289
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12P LOSS MUTATED                                  1
  12P LOSS WILD-TYPE                                6
D64V8, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       59                289
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    51   3   1   4
  12P LOSS WILD-TYPE 264  12   0  15
D64V9, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               51                264
  R1                3                 12
  R2                1                  0
  RX                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0    29
  12P LOSS WILD-TYPE                                1   127
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           4    25
  12P LOSS WILD-TYPE                        13   148
D64V10, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          29                127
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          25                148
[1] 4 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
  12P LOSS MUTATED     3  54
  12P LOSS WILD-TYPE   8 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3   54
  12P LOSS WILD-TYPE    8  275
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               54                275
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    18  10
  12Q LOSS WILD-TYPE 207  99
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                28                306 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                10                 99 
$`12Q LOSS MUTATED`
TCGA-2Y-A9GS TCGA-3K-AAZ8 TCGA-BC-A217 TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A119 
       23.80        13.02        13.84         3.32         0.13         7.33 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A4NI 
       45.11        49.15        13.64        55.69         5.62        26.83 
TCGA-DD-A4NO TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACU TCGA-DD-AAD8 
       73.81        63.48        15.42        42.81        51.52        40.08 
TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVU TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A3I1 
       18.61        35.08        72.39         0.20         0.62         8.12 
TCGA-FV-A496 TCGA-G3-A25Z TCGA-MI-A75G TCGA-ZP-A9D1 
        0.33        21.53        18.38         0.69 

$`12Q LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55         8.61        10.78        10.59         0.66        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       11.08         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       17.98        14.60        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       36.66         0.66         0.07         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 
        4.24         0.10         0.07         0.10        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       11.47        12.95         6.02        33.04        18.35        21.14 
TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       33.14        32.52        90.28        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH 
       75.65        76.41        55.40        12.53        12.00         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO 
       53.19        69.11         0.30         3.52        58.16        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        59.31        51.35        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       42.58        44.22        22.09        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       14.33        66.67        15.58        18.21        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.25        18.15        20.98        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       21.17        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        23.64        25.78        50.33        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       82.62        59.93        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        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         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38        12.03         0.03        81.73         0.39        13.68 
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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        11.24         8.55        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        11.84        13.38        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        19.92        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
        0.76        17.59        19.76        16.44         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        7.04        10.75        10.32        11.34         0.99        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        13.55        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        40.80        79.30        11.21 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.13               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             73.81             120.82 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            18.495             19.315 
[1] "0.1 - 73.8 (18.5)"  "0.0 - 120.8 (19.3)"
[1] "hr=" "1.2"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED        12        9         1          5          2
  12Q LOSS WILD-TYPE     156       75         2         54          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q LOSS MUTATED            0        3         0         0
  12Q LOSS WILD-TYPE          7        0         1         2
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  12                156
  STAGE II                  9                 75
  STAGE III                 1                  2
  STAGE IIIA                5                 54
  STAGE IIIB                2                  6
  STAGE IIIC                0                  7
  STAGE IV                  3                  0
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12Q LOSS MUTATED      13  11   8   1
  12Q LOSS WILD-TYPE   166  80  65  11
D65V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               13                166
  T2                  11                 80
  T3                   8                 65
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    24   0
  12Q LOSS WILD-TYPE 225   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     24    0
  12Q LOSS WILD-TYPE  225    3
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               24                225
  1                0                  3
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    26   2
  12Q LOSS WILD-TYPE 234   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     26    2
  12Q LOSS WILD-TYPE  234    2
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               26                234
  1                2                  2
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     9  24
  12Q LOSS WILD-TYPE 104 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      9   24
  12Q LOSS WILD-TYPE  104  220
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                9                104
  MALE                 24                220
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12Q LOSS MUTATED                         0                       32
  12Q LOSS WILD-TYPE                       2                      316
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12Q LOSS MUTATED                                  1
  12Q LOSS WILD-TYPE                                6
D65V8, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       32                316
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    29   0   1   2
  12Q LOSS WILD-TYPE 286  15   0  17
D65V9, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               29                286
  R1                0                 15
  R2                1                  0
  RX                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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    18
  12Q LOSS WILD-TYPE                                1   138
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           3    12
  12Q LOSS WILD-TYPE                        14   161
D65V10, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          18                138
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          12                161
[1] 4 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
  12Q LOSS MUTATED     2  30
  12Q LOSS WILD-TYPE   9 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   30
  12Q LOSS WILD-TYPE    9  299
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               30                299
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    68  36
  13Q LOSS WILD-TYPE 157  73
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               104                230 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                36                 73 
$`13Q LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-3K-AAZ8 
       23.80        24.89        56.91        18.25        20.81        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W 
       10.78        10.59        37.32        10.13        27.52         2.99 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO 
        5.03        13.84        22.36        17.98        14.60        18.48 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 
        0.66         0.07         2.86         3.19         3.39         0.10 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.07        79.73        83.57        53.33       113.00         2.60 
TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y 
       21.76        12.95         6.02        18.35        55.69         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NN 
       25.81       102.74        30.61        33.14        30.15        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACG 
       73.81        12.26        35.67       114.35        13.48        15.42 
TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS 
       53.19         3.52        58.16        42.81        13.64        59.31 
TCGA-DD-AAD1 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       18.54        40.08        13.97        40.47         3.78        35.67 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AAE0 TCGA-DD-AAE8 
       34.49         0.39        14.89        66.67        18.25        21.83 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-ED-A4XI TCGA-ED-A7PX 
       25.08        23.64        35.08        89.69        12.69         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A3R2 
        0.20        14.04        13.15        11.93        27.88         6.38 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M6 
       13.68        51.06        58.49        25.64        17.10        12.03 
TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-MI-A75G 
        0.89         3.02         2.20        17.06        11.84        18.38 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RC-A7SH 
       20.71        10.85        19.92        21.01        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-AA0U TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CY 
       15.52        17.59        10.75        11.34        13.55        25.71 
TCGA-ZS-A9CE TCGA-ZS-A9CG 
       40.80        11.21 

$`13Q LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
      120.82        40.41        41.33        47.74        11.74        37.25 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AA1C 
       14.99         1.18         8.55         8.61         0.66        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U 
       11.08         1.51        48.99        27.91        46.78        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF 
       25.32        23.34         1.12        69.57        44.42         0.26 
TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5263 TCGA-CC-A1HT 
       12.72        44.81        13.45        36.66         4.24         3.32 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
        0.10         0.13        37.78         7.33         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       45.11        49.15        33.04        13.64        21.14        27.19 
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        90.28        30.97        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       30.51        39.78        56.25       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACO 
       63.48        12.00         6.41        69.11         0.30        61.68 
TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       14.20        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
       47.67         5.62         4.50        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADJ 
       22.09        40.54        40.83        39.52        37.64        35.05 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
       20.91        29.52        15.06        14.33        15.58        18.21 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       18.87        19.30        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
       19.99         4.64        21.17        23.74        18.90        15.72 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS 
       16.37        25.78        50.33        79.07        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A627 
       65.39        49.48        53.69        13.41        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       13.35         9.73        12.82        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        9.96        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        8.12        12.03         0.03         0.33        81.73         0.39 
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-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        25.25        22.95        20.42 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
        7.76         5.98         1.84        11.24         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        9.70         9.17         8.75         2.14         1.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       37.91        20.75        16.83         3.72         2.14        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 
       12.85         0.62        58.88        17.69         3.09        21.04 
TCGA-RC-A7SB TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       19.33        24.13         0.76        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       15.98         7.04        10.32         0.99        12.99        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF 
       45.57        79.30 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            114.35             120.82 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            18.115             19.890 
[1] "0.1 - 114.3 (18.1)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1.2"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED        45       34         1         17          4
  13Q LOSS WILD-TYPE     123       50         2         42          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q LOSS MUTATED            4        1         0         2
  13Q LOSS WILD-TYPE          3        2         1         0
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  45                123
  STAGE II                 34                 50
  STAGE III                 1                  2
  STAGE IIIA               17                 42
  STAGE IIIB                4                  4
  STAGE IIIC                4                  3
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 2                  0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  13Q LOSS MUTATED      47  37  22   9
  13Q LOSS WILD-TYPE   132  54  51   3
D66V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               47                132
  T2                  37                 54
  T3                  22                 51
  T4                   9                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    81   1
  13Q LOSS WILD-TYPE 168   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     81    1
  13Q LOSS WILD-TYPE  168    2
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               81                168
  1                1                  2
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    84   2
  13Q LOSS WILD-TYPE 176   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     84    2
  13Q LOSS WILD-TYPE  176    2
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               84                176
  1                2                  2
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    44  71
  13Q LOSS WILD-TYPE  69 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     44   71
  13Q LOSS WILD-TYPE   69  173
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               44                 69
  MALE                 71                173
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  13Q LOSS MUTATED                         1                      110
  13Q LOSS WILD-TYPE                       1                      238
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  13Q LOSS MUTATED                                  4
  13Q LOSS WILD-TYPE                                3
D66V8, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                      110                238
  HEPATOCHOLANGIOCARCINOMA (MIXED)                4                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    95   8   0   9
  13Q LOSS WILD-TYPE 220   7   1  10
D66V9, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               95                220
  R1                8                  7
  R2                0                  1
  RX                9                 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
  13Q LOSS MUTATED                                  0    54
  13Q LOSS WILD-TYPE                                1   102
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           5    56
  13Q LOSS WILD-TYPE                        12   117
D66V10, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          54                102
  BLACK OR AFRICAN AMERICAN                       5                 12
  WHITE                                          56                117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     3 108
  13Q LOSS WILD-TYPE   8 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3  108
  13Q LOSS WILD-TYPE    8  221
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO              108                221
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    59  32
  14Q LOSS WILD-TYPE 166  77
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                91                243 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                32                 77 
$`14Q LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-5C-A9VG 
       23.80        80.28        24.89        40.41        41.33        10.78 
TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BC-A217 
        0.66        37.32        10.13        27.52         5.03        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A1HT 
        0.26        22.36         0.07         2.86         3.19         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A118 
        0.07         0.10         0.13        79.73        83.57       113.00 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL 
        2.60        21.76        90.71        45.11        33.04        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB 
       55.69         5.62         7.66        13.78        30.61        32.52 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-AA3A TCGA-DD-AACE 
       30.15        26.83        73.81        12.26        13.48        63.48 
TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD5 
       15.42        42.81        59.31        51.52         5.62        44.22 
TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADM 
       22.09        40.83        40.47         3.78        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 
       29.52        14.89        66.67        18.87        19.30        18.25 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAVU TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A7PX 
       16.37        23.64        72.39        53.69        13.41         0.20 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A3RK 
        0.20        13.41         1.84         0.20        19.59        11.93 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M9 
       81.73        13.68        58.49        25.64        17.10         1.84 
TCGA-G3-AAV1 TCGA-G3-AAV7 TCGA-K7-A5RG TCGA-KR-A7K7 TCGA-NI-A8LF TCGA-RC-A7SF 
       11.80         3.02        17.06        13.38        19.92        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.39        15.52        24.13        16.44         0.99        12.99 
TCGA-ZP-A9D2 
       24.43 

$`14Q LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        63.75        83.24        41.79        27.88       120.82 
TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 
       56.91        47.74        18.25        11.74        37.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VH 
       14.99         1.18         8.55        13.02         8.61        10.59 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
       11.97        11.08         1.51        48.99        27.91        46.78 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       44.42        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 
       13.45        36.66         0.66         3.39         4.24         0.10 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA 
       37.78        53.33         7.33         0.46        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.79        75.65        11.47        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        18.35        21.14        27.19        19.76        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 
       70.06        17.59        20.12       102.74       107.11         0.36 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        90.28        30.97        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       29.56       108.76         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACV 
       58.16        61.68        13.64        14.20        51.35        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADG 
       42.58        40.08        40.54        13.97        39.52        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
       35.67        35.05        34.49        15.06        14.33        15.58 
TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.21        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        21.17        21.83        23.74        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        25.78        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       82.62        59.93        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       66.25        65.39        49.48        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
       13.35         9.73        12.82        14.04        13.15        13.35 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
       18.74        19.99        20.61         0.62         9.96        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        60.89        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T 
        6.38        12.03         0.03         0.33         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        25.25        22.95        20.42 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
        7.76        12.03         5.98        11.24         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.17         0.89         8.75         2.14         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
        2.99        37.91        20.75        16.83         3.72         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.84        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        17.69        21.01         3.09        21.04        19.33 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
        0.76        17.59        19.76         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       10.75        10.32        11.34        24.85        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57         0.69        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            113.00             120.82 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             18.25              19.76 
[1] "0.1 - 113.0 (18.2)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED        37       29         0         22          4
  14Q LOSS WILD-TYPE     131       55         3         37          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q LOSS MUTATED            3        2         0         1
  14Q LOSS WILD-TYPE          4        1         1         1
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  37                131
  STAGE II                 29                 55
  STAGE III                 0                  3
  STAGE IIIA               22                 37
  STAGE IIIB                4                  4
  STAGE IIIC                3                  4
  STAGE IV                  2                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  14Q LOSS MUTATED      38  33  28   5
  14Q LOSS WILD-TYPE   141  58  45   7
D67V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1               38                141
  T2                  33                 58
  T3                  28                 45
  T4                   5                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    75   1
  14Q LOSS WILD-TYPE 174   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     75    1
  14Q LOSS WILD-TYPE  174    2
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               75                174
  1                1                  2
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    83   2
  14Q LOSS WILD-TYPE 177   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     83    2
  14Q LOSS WILD-TYPE  177    2
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               83                177
  1                2                  2
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    28  76
  14Q LOSS WILD-TYPE  85 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     28   76
  14Q LOSS WILD-TYPE   85  168
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               28                 85
  MALE                 76                168
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  14Q LOSS MUTATED                         1                      100
  14Q LOSS WILD-TYPE                       1                      248
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  14Q LOSS MUTATED                                  3
  14Q LOSS WILD-TYPE                                4
D67V8, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                      100                248
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    90   5   0   7
  14Q LOSS WILD-TYPE 225  10   1  12
D67V9, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               90                225
  R1                5                 10
  R2                0                  1
  RX                7                 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 LOSS MUTATED                                  0    56
  14Q LOSS WILD-TYPE                                1   100
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           4    42
  14Q LOSS WILD-TYPE                        13   131
D67V10, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          56                100
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          42                131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     4  94
  14Q LOSS WILD-TYPE   7 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4   94
  14Q LOSS WILD-TYPE    7  235
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               94                235
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    29  23
  15Q LOSS WILD-TYPE 196  86
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                52                282 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                23                 86 
$`15Q LOSS MUTATED`
TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-BC-A112 TCGA-BC-A5W4 TCGA-BC-A69H 
       20.81        13.02        10.59         5.03        17.98        14.60 
TCGA-CC-5258 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11A 
        0.07         0.07        79.73        37.78        83.57         2.60 
TCGA-DD-A1E9 TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 
       90.71         6.02        33.04        13.64         5.62       102.74 
TCGA-DD-A4NA TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACG TCGA-DD-AACL 
       33.14        12.26         9.30         0.53        15.42         3.52 
TCGA-DD-AADB TCGA-DD-AADK TCGA-DD-AADO TCGA-DD-AAE1 TCGA-DD-AAVQ TCGA-ED-A459 
       40.83        34.49        14.89        18.15        89.69        13.41 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KB TCGA-FV-A496 
        9.73         0.20         0.20        13.41        19.59         0.33 
TCGA-FV-A4ZP TCGA-G3-A25Z TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV4 
       81.73        21.53        17.10         1.84        11.80         0.89 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-RG-A7D4 
        2.14         3.02        17.06        11.84        13.38        24.13 
TCGA-UB-A7MA TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CF 
       17.59         0.99        13.55        79.30 

$`15Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       47.74        18.25        11.74        37.25        14.99         1.18 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55         8.61        10.78         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        1.51        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I 
       69.57        44.42        13.84         0.26        22.36        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 
       18.48        44.81        13.45        36.66         0.66         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
        3.19         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        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       12.95        45.11        49.15        18.35        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB 
       20.12       107.11        13.78         0.36        30.61        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       90.28        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      114.35        13.48        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        63.48        12.00         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        0.30        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD 
       44.22        22.09        40.08        40.54        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADL 
       39.52         3.78        37.64        35.67        35.05        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 
       18.21        18.87        19.30        18.25        18.25        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       18.90        15.72        25.08        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        35.08        79.07        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        53.69        12.69        15.85        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       12.82        14.04        13.15        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        20.61         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        60.89        23.97        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        12.03         0.03         0.39        13.68 
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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       22.95        20.42         7.76        12.03         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        8.55         9.70         9.17         8.75         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
        2.99        37.91        20.75        16.83         3.72         2.14 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       18.38        12.85        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       19.92        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        15.52         0.76        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
        1.71        15.98         7.04        10.75        10.32        11.34 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       12.99        24.85        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
        0.69        24.43        12.99        45.57        40.80        11.21 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.07               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            102.74             120.82 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             13.48              20.27 
[1] "0.1 - 102.7 (13.5)" "0.0 - 120.8 (20.3)"
[1] "hr=" "1.7"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  15Q LOSS MUTATED        19       21         1         15          2
  15Q LOSS WILD-TYPE     149       63         2         44          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q LOSS MUTATED            3        0         0         0
  15Q LOSS WILD-TYPE          4        3         1         2
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  19                149
  STAGE II                 21                 63
  STAGE III                 1                  2
  STAGE IIIA               15                 44
  STAGE IIIB                2                  6
  STAGE IIIC                3                  4
  STAGE IV                  0                  3
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  15Q LOSS MUTATED      21  21  20   1
  15Q LOSS WILD-TYPE   158  70  53  11
D68V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1               21                158
  T2                  21                 70
  T3                  20                 53
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    43   2
  15Q LOSS WILD-TYPE 206   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     43    2
  15Q LOSS WILD-TYPE  206    1
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               43                206
  1                2                  1
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    54   0
  15Q LOSS WILD-TYPE 206   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     54    0
  15Q LOSS WILD-TYPE  206    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               54                206
  1                0                  4
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    20  43
  15Q LOSS WILD-TYPE  93 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     20   43
  15Q LOSS WILD-TYPE   93  201
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               20                 93
  MALE                 43                201
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  15Q LOSS MUTATED                         0                       61
  15Q LOSS WILD-TYPE                       2                      287
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  15Q LOSS MUTATED                                  2
  15Q LOSS WILD-TYPE                                5
D68V8, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       61                287
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    56   3   0   4
  15Q LOSS WILD-TYPE 259  12   1  15
D68V9, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               56                259
  R1                3                 12
  R2                0                  1
  RX                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0    30
  15Q LOSS WILD-TYPE                                1   126
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           6    27
  15Q LOSS WILD-TYPE                        11   146
D68V10, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          30                126
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          27                146
[1] 4 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
  15Q LOSS MUTATED     3  57
  15Q LOSS WILD-TYPE   8 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3   57
  15Q LOSS WILD-TYPE    8  272
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               57                272
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    63  31
  16P LOSS WILD-TYPE 162  78
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                94                240 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                31                 78 
$`16P LOSS MUTATED`
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-BC-A217 TCGA-BC-A5W4 
       56.91        41.33        37.25        20.81        13.84        17.98 
TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       14.60        13.45         0.66         0.07         2.86         3.19 
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        33.04         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        90.28        30.15        26.83        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL 
       73.81        12.26         9.30        55.40        15.42         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
       58.16        42.81        13.64        59.31        51.52        46.82 
TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI TCGA-DD-AADJ 
        5.62        42.58        40.54        40.83        35.67        35.05 
TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY 
       20.91        14.89        15.06        66.67        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEK 
       18.25        18.15         4.64        21.83        25.08        35.08 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVZ TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       59.93        72.39        62.47        15.85        13.35         9.73 
TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B 
       12.82        13.35         1.84        19.59        22.85        60.89 
TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A7M9 
       23.97        27.88         6.38        58.49        14.86         1.84 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-QA-A7B7 
        2.14         3.02        13.38        18.38        20.71         3.09 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MF 
       19.33        15.39        24.13         0.76        17.59         7.04 
TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZS-A9CG 
        0.99        13.55         0.69        11.21 

$`16P LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       24.89        27.88       120.82        40.41        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       11.74        14.99         1.18         8.55        13.02         8.61 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        11.97        11.08         1.51 
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-BC-A8YO 
        5.03        44.42         0.26        22.36        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A113 
       44.81        36.66         4.24         3.32         0.07        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
       83.57        53.33       113.00         7.33         2.60        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       11.47        45.11        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        13.78        33.14        32.52        30.97 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       30.51        39.78        56.25       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        63.48        12.00         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACX 
        0.30        61.68        14.20        51.35        50.33         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 
       47.67         4.50        18.54        21.63        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.08        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
       34.49         0.39        29.52        14.33        15.58        18.21 
TCGA-DD-AADV TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 
       18.87        20.98        18.61        19.99        21.17        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       18.90        15.72        16.37        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       79.07        89.69        82.62        76.18        56.48        64.77 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        13.41        12.69 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.91         0.20         0.20        14.04        13.15        13.41 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        20.61         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       11.93        14.40        19.10         8.12        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        81.73         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        30.74        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        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
        7.76        12.03         5.98        11.24         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.70         9.17         0.89         8.75         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        11.84        24.36        12.72        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        12.85         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK 
       19.92        17.69        21.01        21.04        19.04        15.52 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V 
       19.76        16.44         1.71        15.98        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       11.34        12.99        24.85        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57        24.43        12.99        45.57        40.80        79.30 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             90.28             120.82 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            18.065             19.955 
[1] "0.1 - 90.3 (18.1)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.2"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P LOSS MUTATED        42       32         1         20          3
  16P LOSS WILD-TYPE     126       52         2         39          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P LOSS MUTATED            3        1         1         1
  16P LOSS WILD-TYPE          4        2         0         1
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  42                126
  STAGE II                 32                 52
  STAGE III                 1                  2
  STAGE IIIA               20                 39
  STAGE IIIB                3                  5
  STAGE IIIC                3                  4
  STAGE IV                  1                  2
  STAGE IVA                 1                  0
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16P LOSS MUTATED      47  33  24   4
  16P LOSS WILD-TYPE   132  58  49   8
D69V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1               47                132
  T2                  33                 58
  T3                  24                 49
  T4                   4                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    81   2
  16P LOSS WILD-TYPE 168   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     81    2
  16P LOSS WILD-TYPE  168    1
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               81                168
  1                2                  1
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    88   2
  16P LOSS WILD-TYPE 172   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     88    2
  16P LOSS WILD-TYPE  172    2
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               88                172
  1                2                  2
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    39  69
  16P LOSS WILD-TYPE  74 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     39   69
  16P LOSS WILD-TYPE   74  175
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               39                 74
  MALE                 69                175
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16P LOSS MUTATED                         0                      106
  16P LOSS WILD-TYPE                       2                      242
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16P LOSS MUTATED                                  2
  16P LOSS WILD-TYPE                                5
D69V8, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                      106                242
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    95   2   0  10
  16P LOSS WILD-TYPE 220  13   1   9
D69V9, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               95                220
  R1                2                 13
  R2                0                  1
  RX               10                  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
  16P LOSS MUTATED                                  0    62
  16P LOSS WILD-TYPE                                1    94
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           6    39
  16P LOSS WILD-TYPE                        11   134
D69V10, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          62                 94
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          39                134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     5 100
  16P LOSS WILD-TYPE   6 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5  100
  16P LOSS WILD-TYPE    6  229
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  6
  NOT HISPANIC OR LATINO              100                229
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    86  41
  16Q LOSS WILD-TYPE 139  68
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               127                207 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                41                 68 
$`16Q LOSS MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 
       24.89        56.91        41.33        18.25        37.25        20.81 
TCGA-2Y-A9HA TCGA-5C-AAPD TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 
        1.18         0.66        46.78         2.99        44.42        13.84 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       22.36        14.60        18.48        13.45         0.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        2.86         3.19         4.24         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EH 
       37.78        53.33         2.60         0.46        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A8 TCGA-DD-A3A9 
        6.02        33.04         5.62        19.76         0.36        30.61 
TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       90.28        30.15        26.83        29.56        73.81        12.26 
TCGA-DD-A73B TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
        9.30        55.40        12.00        15.42         6.41        53.19 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD3 
       59.31        51.52        46.82         5.62        18.54        42.58 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       40.54        40.83        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY 
        0.39        14.89        15.06        66.67        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEH 
       18.25        18.15         4.64        21.83        25.08        25.78 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ 
       35.08        89.69        59.93        72.39        76.18        62.47 
TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       66.25        13.41        15.85        13.35         9.73        12.82 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ 
       13.35         1.84        19.59        22.85        60.89        23.97 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y 
       27.88         6.38        13.68        53.79        58.49        14.86 
TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV6 TCGA-G3-AAV7 
       25.64        25.25         1.84        11.24         2.14         3.02 
TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SB 
       13.38        18.38        20.71        17.69         3.09        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        24.13         0.76        17.59        19.76 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-ZP-A9CZ TCGA-ZP-A9D1 
        7.04        10.75        11.34         0.99        23.21         0.69 
TCGA-ZS-A9CG 
       11.21 

$`16Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H9 
       27.88       120.82        40.41        47.74        11.74        14.99 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C 
        8.55        13.02         8.61        10.78        10.59        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       11.08         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52        27.52        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3ER 
        5.03         0.26        17.98        12.72        44.81        36.66 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 
        3.39         3.32         0.10         0.07        83.57       113.00 
TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL 
       19.79        75.65        11.47        45.11        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        55.69        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       32.52        30.97        30.51        39.78        56.25       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        23.93        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACK 
       75.65        76.41        12.53        63.48        69.11         0.30 
TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD2 
       51.35        50.33         5.59        47.67         4.50        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       44.22        22.09        40.08        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
        3.78        37.64        29.52        14.33        15.58        18.21 
TCGA-DD-AADV TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 
       18.87        20.98        18.61        19.99        21.17        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAVP 
       18.90        15.72        16.37        23.64        50.33        79.07 
TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       82.62        56.48        64.77        65.39        49.48        53.69 
TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       12.69        13.91         0.20         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       13.41         0.20        18.74        19.99        20.61         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 
        9.96        11.93        14.40        19.10         8.12        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V 
        0.03         0.33        81.73         0.39        51.06        28.27 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       30.74        21.53        22.13         5.92        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
        8.55        11.80         9.70         9.17         0.89         8.75 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG 
       16.83         3.72         2.14        11.84        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 
       13.97        12.03         9.57        16.67        12.85         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SK 
       10.85        58.88        19.92        21.01        21.04        15.52 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WQ-AB4B TCGA-WX-AA46 
       16.44         1.71        15.98        10.32        12.99        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       13.55        35.77        25.71        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       45.57        40.80        79.30 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             90.28             120.82 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             18.48              19.92 
[1] "0.1 - 90.3 (18.5)"  "0.0 - 120.8 (19.9)"
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED        57       46         1         23          3
  16Q LOSS WILD-TYPE     111       38         2         36          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q LOSS MUTATED            3        1         1         1
  16Q LOSS WILD-TYPE          4        2         0         1
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  57                111
  STAGE II                 46                 38
  STAGE III                 1                  2
  STAGE IIIA               23                 36
  STAGE IIIB                3                  5
  STAGE IIIC                3                  4
  STAGE IV                  1                  2
  STAGE IVA                 1                  0
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16Q LOSS MUTATED      63  47  28   5
  16Q LOSS WILD-TYPE   116  44  45   7
D70V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               63                116
  T2                  47                 44
  T3                  28                 45
  T4                   5                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   107   2
  16Q LOSS WILD-TYPE 142   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    107    2
  16Q LOSS WILD-TYPE  142    1
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              107                142
  1                2                  1
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   114   2
  16Q LOSS WILD-TYPE 146   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    114    2
  16Q LOSS WILD-TYPE  146    2
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              114                146
  1                2                  2
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    50  93
  16Q LOSS WILD-TYPE  63 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     50   93
  16Q LOSS WILD-TYPE   63  151
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               50                 63
  MALE                 93                151
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16Q LOSS MUTATED                         0                      140
  16Q LOSS WILD-TYPE                       2                      208
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16Q LOSS MUTATED                                  3
  16Q LOSS WILD-TYPE                                4
D70V8, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                      140                208
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED   126   6   0  11
  16Q LOSS WILD-TYPE 189   9   1   8
D70V9, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0              126                189
  R1                6                  9
  R2                0                  1
  RX               11                  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
  16Q LOSS MUTATED                                  0    84
  16Q LOSS WILD-TYPE                                1    72
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           7    49
  16Q LOSS WILD-TYPE                        10   124
D70V10, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          84                 72
  BLACK OR AFRICAN AMERICAN                       7                 10
  WHITE                                          49                124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     6 133
  16Q LOSS WILD-TYPE   5 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      6  133
  16Q LOSS WILD-TYPE    5  196
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  5
  NOT HISPANIC OR LATINO              133                196
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   100  61
  17P LOSS WILD-TYPE 125  48
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               161                173 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                61                 48 
$`17P LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       23.80        53.39        83.24        24.89        27.88       120.82 
TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-5C-AAPD 
       56.91        18.25        20.81        14.99         1.18         0.66 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10Y 
        1.51        48.99        27.91        10.13        27.52        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57         5.03        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 
       17.98        14.60        18.48        44.81        13.45         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB 
        2.86         3.19         3.39         4.24         3.32         0.10 
TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        0.13        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EH 
       21.76        51.29        79.40        66.31        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 
        6.02        33.04        18.35        13.64         5.62        25.81 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH 
       17.59        20.12       102.74        33.14        32.52        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-AACA 
       26.83        30.51        12.26         9.30         1.45        75.65 
TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACL 
       55.40        63.48        15.42         6.41        69.11         3.52 
TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD3 
       58.16        14.20         5.59         5.62        18.54        42.58 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF 
       22.09        40.08        40.83        13.97        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW 
       37.64        20.91        29.52        66.67        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAEA 
       18.25        18.25        20.98        19.99         4.64        18.90 
TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.72        16.37        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ 
       82.62        72.39        65.39        13.41         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A23B TCGA-FV-A2QQ 
       13.41         1.84         0.20         0.62        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
       19.10        27.88         0.03        13.68        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 
       14.86        21.53        25.64        20.42        17.10        12.03 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
        1.84        11.24        11.80         0.89         8.75         3.02 
TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG 
        1.02        37.91         3.72         2.14        11.84        12.72 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 
       16.67        18.38        20.71        58.88        17.69         3.09 
TCGA-RC-A7SB TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC 
       19.33        15.52        24.13         0.76        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 
        1.71        15.98         7.04        11.34        12.99        13.55 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        40.80        79.30 

$`17P LOSS WILD-TYPE`
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       63.75        41.79        80.28        40.41        41.33        47.74 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG 
       11.74        37.25         8.55        13.02         8.61        10.78 
TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T 
       10.59        11.97        11.08        37.32        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A216 TCGA-BC-A69I TCGA-BD-A3ER TCGA-BW-A5NO 
        2.99        25.32        44.42        12.72        36.66         0.66 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A1E9 
        0.10         0.07        79.73        37.78         0.46        90.71 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39W 
       19.79        75.65        11.47        12.95        21.14        27.19 
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        90.28        30.97        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        73.81       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.93        23.05        22.78        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI 
        0.53        11.41        76.41        12.53        12.00        53.19 
TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT 
        0.30        42.81        61.68        13.64        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD2 
       51.52        50.33        46.82        47.67         4.50        21.63 
TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       44.22        40.54        40.47        35.67        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
        0.39        14.89        15.06        14.33        15.58        18.21 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAED 
       18.15        18.61        21.17        21.83        23.74        25.08 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       23.64        25.78        59.93        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       62.47        66.25        49.48        53.69        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91        13.35         9.73        12.82        14.04        13.15 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
       13.35        18.74        19.99        20.61        19.59         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        12.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X 
        0.33        81.73         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        25.25        22.95 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 
        7.76         5.98         8.55         9.70         9.17         2.14 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K7 
        2.20         2.99        20.75        17.06        16.83        13.38 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H TCGA-MR-A520 
       24.36        13.97        12.03         9.57        12.85         0.62 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
       10.85        19.92        21.01        21.04        19.04        15.39 
TCGA-UB-A7MA TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-ZP-A9CV 
       17.59        10.75        10.32         0.99        24.85        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       25.71        23.21        23.57        45.57        11.21 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            120.82             114.35 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             18.35              20.61 
[1] "0.0 - 120.8 (18.4)" "0.1 - 114.3 (20.6)"
[1] "hr=" "1.5"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED        67       48         2         33          3
  17P LOSS WILD-TYPE     101       36         1         26          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P LOSS MUTATED            7        3         1         1
  17P LOSS WILD-TYPE          0        0         0         1
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  67                101
  STAGE II                 48                 36
  STAGE III                 2                  1
  STAGE IIIA               33                 26
  STAGE IIIB                3                  5
  STAGE IIIC                7                  0
  STAGE IV                  3                  0
  STAGE IVA                 1                  0
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17P LOSS MUTATED      74  54  40   8
  17P LOSS WILD-TYPE   105  37  33   4
D71V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               74                105
  T2                  54                 37
  T3                  40                 33
  T4                   8                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   123   3
  17P LOSS WILD-TYPE 126   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    123    3
  17P LOSS WILD-TYPE  126    0
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              123                126
  1                3                  0
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   131   3
  17P LOSS WILD-TYPE 129   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    131    3
  17P LOSS WILD-TYPE  129    1
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              131                129
  1                3                  1
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    57 120
  17P LOSS WILD-TYPE  56 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     57  120
  17P LOSS WILD-TYPE   56  124
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               57                 56
  MALE                120                124
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17P LOSS MUTATED                         1                      171
  17P LOSS WILD-TYPE                       1                      177
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17P LOSS MUTATED                                  5
  17P LOSS WILD-TYPE                                2
D71V8, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                      171                177
  HEPATOCHOLANGIOCARCINOMA (MIXED)                5                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   154   7   1  13
  17P LOSS WILD-TYPE 161   8   0   6
D71V9, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              154                161
  R1                7                  8
  R2                1                  0
  RX               13                  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
  17P LOSS MUTATED                                  0    84
  17P LOSS WILD-TYPE                                1    72
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           9    80
  17P LOSS WILD-TYPE                         8    93
D71V10, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          84                 72
  BLACK OR AFRICAN AMERICAN                       9                  8
  WHITE                                          80                 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"
D71V11, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     8 161
  17P LOSS WILD-TYPE   3 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      8  161
  17P LOSS WILD-TYPE    3  168
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  3
  NOT HISPANIC OR LATINO              161                168
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    19  14
  17Q LOSS WILD-TYPE 206  95
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                33                301 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                14                 95 
$`17Q LOSS MUTATED`
TCGA-2Y-A9GZ TCGA-2Y-A9H5 TCGA-BC-A10R TCGA-BC-A5W4 TCGA-BD-A3EP TCGA-DD-A1EB 
       27.88        18.25        10.13        17.98        13.45        66.31 
TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A3A0 TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI 
       45.11        33.04        25.81        32.52        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-AACH TCGA-DD-AACZ TCGA-DD-AAE0 TCGA-DD-AAEK TCGA-ED-A82E 
       30.51         6.41         5.62        18.25        35.08        13.41 
TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M9 
        0.20        23.97        27.88        20.42        17.10         1.84 
TCGA-G3-AAV1 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MF 
       11.80         2.14        11.84        24.13         0.76         7.04 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 
       12.99        13.55         0.69 

$`17Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       24.89       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        37.25        20.81        14.99         1.18         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
       13.02         8.61        10.78        10.59         0.66        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
       11.08         1.51        48.99        27.91        37.32        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       69.57         5.03        44.42        13.84         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-BW-A5NO 
       14.60        12.72        18.48        44.81        36.66         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.19         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        90.71        79.40        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       11.47        12.95        49.15         6.02        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 
       21.14        27.19        55.69         5.62        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK 
        0.36        30.61        33.14        90.28        30.97        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        18.87        19.30        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       18.90        15.72        25.08        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.15        13.35         1.84        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.59         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        19.10         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        81.73         0.39        13.68        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        25.25        22.95 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
        7.76        12.03         5.98        11.24         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.17         0.89         8.75         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.91        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
        3.72        13.38        24.36        12.72        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
        9.57        16.67        18.38        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        19.92        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA 
       21.04        19.33        19.04        15.39        15.52        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V 
       19.76        16.44         1.71        15.98        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       11.34         0.99        24.85        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57        24.43        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             66.31             120.82 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             17.98              19.53 
[1] "0.2 - 66.3 (18.0)"  "0.0 - 120.8 (19.5)"
[1] "hr=" "1.9"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q LOSS MUTATED         9       10         0          9          2
  17Q LOSS WILD-TYPE     159       74         3         50          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q LOSS MUTATED            2        1         1         0
  17Q LOSS WILD-TYPE          5        2         0         2
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   9                159
  STAGE II                 10                 74
  STAGE III                 0                  3
  STAGE IIIA                9                 50
  STAGE IIIB                2                  6
  STAGE IIIC                2                  5
  STAGE IV                  1                  2
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17Q LOSS MUTATED      13  11  12   1
  17Q LOSS WILD-TYPE   166  80  61  11
D72V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1               13                166
  T2                  11                 80
  T3                  12                 61
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    22   2
  17Q LOSS WILD-TYPE 227   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     22    2
  17Q LOSS WILD-TYPE  227    1
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               22                227
  1                2                  1
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    28   1
  17Q LOSS WILD-TYPE 232   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     28    1
  17Q LOSS WILD-TYPE  232    3
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               28                232
  1                1                  3
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    15  22
  17Q LOSS WILD-TYPE  98 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     15   22
  17Q LOSS WILD-TYPE   98  222
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               15                 98
  MALE                 22                222
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17Q LOSS MUTATED                         1                       33
  17Q LOSS WILD-TYPE                       1                      315
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17Q LOSS MUTATED                                  3
  17Q LOSS WILD-TYPE                                4
D72V8, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       33                315
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    34   1   0   2
  17Q LOSS WILD-TYPE 281  14   1  17
D72V9, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               34                281
  R1                1                 14
  R2                0                  1
  RX                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0    10
  17Q LOSS WILD-TYPE                                1   146
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           2    24
  17Q LOSS WILD-TYPE                        15   149
D72V10, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          10                146
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          24                149
[1] 4 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
  17Q LOSS MUTATED     2  32
  17Q LOSS WILD-TYPE   9 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   32
  17Q LOSS WILD-TYPE    9  297
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               32                297
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    45  20
  18P LOSS WILD-TYPE 180  89
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                65                269 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                20                 89 
$`18P LOSS MUTATED`
TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-A10R TCGA-BC-A112 
       41.33        20.81         0.66        11.08        10.13         5.03 
TCGA-BC-A217 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF 
       13.84         0.10       113.00         2.60         0.46        12.95 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A4 TCGA-DD-A4NB 
       33.04        13.64        55.69         5.62        20.12        32.52 
TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB 
       26.83        73.81         1.45       114.35         0.53        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO 
       55.40        12.53        63.48        53.19        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
       13.64        50.33         5.62        44.22        22.09        40.54 
TCGA-DD-AADI TCGA-DD-AADO TCGA-DD-AAE2 TCGA-DD-AAEG TCGA-DD-AAEK TCGA-ED-A459 
       35.67        14.89        20.98        23.64        35.08        13.41 
TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A3I0 
        0.20        13.15        13.41         1.84        22.85        27.88 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K7 TCGA-MI-A75G 
        0.33        13.68        11.80         2.14        13.38        18.38 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-RC-A7SF TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA 
       10.85        19.92        19.04        15.52         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-YA-A8S7 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       19.76        16.44        13.55        40.80        11.21 

$`18P LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 
       24.89        27.88       120.82        40.41        56.91        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       18.25        11.74        37.25        14.99         1.18         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AAAM 
       13.02         8.61        10.78        10.59        11.97         1.51 
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-BC-A8YO 
        0.26        22.36        17.98        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       44.81        13.45        36.66         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.19         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        11.47        45.11        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        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        90.28        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       78.84        23.93         9.30        23.05        22.78        35.67 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       13.48        11.41        75.65        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS 
       69.11         0.30         3.52        58.16        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.35        51.52        46.82         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       18.54        21.63        42.58        40.08        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52         3.78        37.64        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91         0.39        29.52        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       15.58        18.21        18.87        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.15        18.61        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
       23.74        18.90        15.72        25.08        16.37        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        53.69        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K 
        9.73        12.82         0.20        14.04        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       11.93        14.40        60.89        23.97        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
        6.38        12.03         0.03        81.73         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83         3.72         2.14        11.84 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       12.85        20.71         0.62        58.88        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MD 
        3.09        21.04        19.33        15.39        24.13         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.98         7.04        10.75        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       12.99        24.85        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        79.30 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.10               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            114.35             120.82 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             16.44              19.59 
[1] "0.1 - 114.3 (16.4)" "0.0 - 120.8 (19.6)"
[1] "hr=" "1"  
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED        33       20         0         11          0
  18P LOSS WILD-TYPE     135       64         3         48          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P LOSS MUTATED            2        1         0         0
  18P LOSS WILD-TYPE          5        2         1         2
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  33                135
  STAGE II                 20                 64
  STAGE III                 0                  3
  STAGE IIIA               11                 48
  STAGE IIIB                0                  8
  STAGE IIIC                2                  5
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18P LOSS MUTATED      36  20  13   1
  18P LOSS WILD-TYPE   143  71  60  11
D73V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               36                143
  T2                  20                 71
  T3                  13                 60
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    51   1
  18P LOSS WILD-TYPE 198   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     51    1
  18P LOSS WILD-TYPE  198    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               51                198
  1                1                  2
[1] 2 2
[1] FALSE
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    56   1
  18P LOSS WILD-TYPE 204   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     56    1
  18P LOSS WILD-TYPE  204    3
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               56                204
  1                1                  3
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    26  44
  18P LOSS WILD-TYPE  87 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     26   44
  18P LOSS WILD-TYPE   87  200
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               26                 87
  MALE                 44                200
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18P LOSS MUTATED                         2                       65
  18P LOSS WILD-TYPE                       0                      283
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18P LOSS MUTATED                                  3
  18P LOSS WILD-TYPE                                4
D73V8, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       65                283
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    63   2   0   5
  18P LOSS WILD-TYPE 252  13   1  14
D73V9, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               63                252
  R1                2                 13
  R2                0                  1
  RX                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0    33
  18P LOSS WILD-TYPE                                1   123
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           2    35
  18P LOSS WILD-TYPE                        15   138
D73V10, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          33                123
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          35                138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  64
  18P LOSS WILD-TYPE   8 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   64
  18P LOSS WILD-TYPE    8  265
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               64                265
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    48  19
  18Q LOSS WILD-TYPE 177  90
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                67                267 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                19                 90 
$`18Q LOSS MUTATED`
TCGA-2Y-A9H3 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-A10R TCGA-BC-A112 
       41.33        10.59         0.66        11.08        10.13         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       44.42        13.84         0.10       113.00         2.60         0.46 
TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 
       12.95        33.04        13.64        55.69         5.62        30.61 
TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-A73G 
       32.52        26.83        73.81         9.30         1.45       114.35 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO 
        0.53        76.41        63.48        53.19        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADA 
       13.64        50.33         5.59         5.62        22.09        40.54 
TCGA-DD-AADI TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAEG TCGA-DD-AAEK 
       35.67        14.89        19.30        20.98        23.64        35.08 
TCGA-DD-AAVP TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
       79.07        13.41        13.35        13.15        13.41         1.84 
TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-AAV1 TCGA-G3-AAV6 
       22.85        27.88         0.33        13.68        11.80         2.14 
TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MR-A8JO TCGA-NI-A8LF TCGA-RC-A7SF TCGA-RC-A7SK 
       13.38        18.38        10.85        19.92        19.04        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MF TCGA-YA-A8S7 TCGA-ZS-A9CE 
       24.13         0.76        16.44         7.04        13.55        40.80 
TCGA-ZS-A9CG 
       11.21 

$`18Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 
       24.89        27.88       120.82        40.41        56.91        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5R-AA1C TCGA-5R-AAAM 
        8.55        13.02         8.61        10.78        11.97         1.51 
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-BC-A8YO TCGA-BD-A2L6 
       22.36        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.45        36.66         0.66         0.07         2.86         3.19 
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-A11C 
       79.73        37.78        83.57        53.33         7.33        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-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V 
       11.47        45.11        49.15         6.02        18.35        21.14 
TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        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 
       90.28        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 
       23.93        23.05        22.78        35.67        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       75.65        55.40        12.53        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS 
       69.11         0.30         3.52        58.16        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 
       51.35        51.52        46.82        47.67         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       21.63        42.58        44.22        40.08        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52         3.78        37.64        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91         0.39        29.52        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        18.87        18.25        18.25        18.15 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       18.90        15.72        25.08        16.37        25.78        50.33 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       12.69        15.85        13.91         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
        0.20        14.04        13.35         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       20.61        19.59         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       60.89        23.97        19.10         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03        81.73         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        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
        8.55         9.70         9.17         0.89         8.75         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG 
       16.83         3.72         2.14        11.84        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        12.85        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
        0.62        58.88        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       19.33        15.39        17.59        19.76         1.71        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       10.75        10.32        11.34         0.99        12.99        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       12.99        45.57        79.30 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.10               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            114.35             120.82 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             14.89              19.76 
[1] "0.1 - 114.3 (14.9)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED        35       18         0         13          0
  18Q LOSS WILD-TYPE     133       66         3         46          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q LOSS MUTATED            2        1         0         1
  18Q LOSS WILD-TYPE          5        2         1         1
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  35                133
  STAGE II                 18                 66
  STAGE III                 0                  3
  STAGE IIIA               13                 46
  STAGE IIIB                0                  8
  STAGE IIIC                2                  5
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18Q LOSS MUTATED      37  19  15   2
  18Q LOSS WILD-TYPE   142  72  58  10
D74V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               37                142
  T2                  19                 72
  T3                  15                 58
  T4                   2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    54   1
  18Q LOSS WILD-TYPE 195   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     54    1
  18Q LOSS WILD-TYPE  195    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               54                195
  1                1                  2
[1] 2 2
[1] FALSE
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    58   2
  18Q LOSS WILD-TYPE 202   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     58    2
  18Q LOSS WILD-TYPE  202    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               58                202
  1                2                  2
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    26  47
  18Q LOSS WILD-TYPE  87 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     26   47
  18Q LOSS WILD-TYPE   87  197
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               26                 87
  MALE                 47                197
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18Q LOSS MUTATED                         2                       69
  18Q LOSS WILD-TYPE                       0                      279
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18Q LOSS MUTATED                                  2
  18Q LOSS WILD-TYPE                                5
D74V8, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       69                279
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED    67   1   0   5
  18Q LOSS WILD-TYPE 248  14   1  14
D74V9, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               67                248
  R1                1                 14
  R2                0                  1
  RX                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0    34
  18Q LOSS WILD-TYPE                                1   122
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           3    36
  18Q LOSS WILD-TYPE                        14   137
D74V10, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          34                122
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          36                137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4  65
  18Q LOSS WILD-TYPE   7 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4   65
  18Q LOSS WILD-TYPE    7  264
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               65                264
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    27  18
  19P LOSS WILD-TYPE 198  91
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                45                289 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                18                 91 
$`19P LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       23.80        24.89        27.88       120.82        56.91        41.33 
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        33.04         5.62        30.51 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU 
       63.48        15.42        61.68        13.64        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADV 
       50.33         5.62        13.97        40.47        20.91        18.87 
TCGA-DD-AAE8 TCGA-DD-AAVR TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A496 TCGA-FV-A4ZP 
       21.83        82.62         1.84         0.20         0.33        81.73 
TCGA-G3-A25S TCGA-G3-A3CH TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-RC-A7SK TCGA-RG-A7D4 
       13.68        25.64        12.03        11.80        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-ZP-A9CV 
        0.76        17.59        35.77 

$`19P LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H1 
       53.39        63.75        83.24        41.79        80.28        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
        0.66        11.97        11.08         1.51        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       37.32        10.13        46.78        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       23.34         1.12        69.57        44.42        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       17.98        14.60        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 
       36.66         0.66         2.86         3.19         3.39         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       12.95        49.15        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        90.28        30.97        30.15        26.83 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       11.41        75.65        76.41        55.40        12.53        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       42.81        14.20        51.35        46.82         5.59        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.08        40.54        40.83        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.67        35.05        34.49         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        21.17        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       16.37        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       89.69        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        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         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        60.89        23.97        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        12.03         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-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        22.13         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
       22.95        20.42        17.10         7.76         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       11.24         8.55         9.70         9.17         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83         3.72         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        19.92        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       19.33        19.04        15.39        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.98         7.04        10.75        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       12.99        24.85        13.55        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.07               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            120.82             114.35 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             18.87              19.30 
[1] "0.1 - 120.8 (18.9)" "0.0 - 114.3 (19.3)"
[1] "hr=" "1.3"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED        24        9         0         12          1
  19P LOSS WILD-TYPE     144       75         3         47          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P LOSS MUTATED            2        1         0         0
  19P LOSS WILD-TYPE          5        2         1         2
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  24                144
  STAGE II                  9                 75
  STAGE III                 0                  3
  STAGE IIIA               12                 47
  STAGE IIIB                1                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19P LOSS MUTATED      27  10  13   3
  19P LOSS WILD-TYPE   152  81  60   9
D75V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               27                152
  T2                  10                 81
  T3                  13                 60
  T4                   3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    38   1
  19P LOSS WILD-TYPE 211   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     38    1
  19P LOSS WILD-TYPE  211    2
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               38                211
  1                1                  2
[1] 2 2
[1] FALSE
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    43   0
  19P LOSS WILD-TYPE 217   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     43    0
  19P LOSS WILD-TYPE  217    4
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               43                217
  1                0                  4
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    12  41
  19P LOSS WILD-TYPE 101 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     12   41
  19P LOSS WILD-TYPE  101  203
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               12                101
  MALE                 41                203
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19P LOSS MUTATED                         0                       51
  19P LOSS WILD-TYPE                       2                      297
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19P LOSS MUTATED                                  2
  19P LOSS WILD-TYPE                                5
D75V8, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       51                297
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    44   4   0   4
  19P LOSS WILD-TYPE 271  11   1  15
D75V9, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               44                271
  R1                4                 11
  R2                0                  1
  RX                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0    32
  19P LOSS WILD-TYPE                                1   124
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           2    19
  19P LOSS WILD-TYPE                        15   154
D75V10, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          32                124
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          19                154
[1] 4 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
  19P LOSS MUTATED     3  49
  19P LOSS WILD-TYPE   8 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3   49
  19P LOSS WILD-TYPE    8  280
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               49                280
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    19  11
  19Q LOSS WILD-TYPE 206  98
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                30                304 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                11                 98 
$`19Q LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-BC-A112 TCGA-BC-A3KF 
       23.80        24.89        27.88       120.82         5.03         0.26 
TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT TCGA-DD-A11A TCGA-DD-A1EI TCGA-DD-A1EJ 
        0.07         4.24         3.32         2.60         6.02        33.04 
TCGA-DD-A39Y TCGA-DD-A4NJ TCGA-DD-AACE TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
        5.62        30.51        63.48        59.31        51.52        50.33 
TCGA-DD-AADL TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAVR TCGA-DD-AAVW TCGA-ED-A8O6 
       20.91        18.87        21.83        82.62        76.18         1.84 
TCGA-FV-A4ZP TCGA-G3-AAV1 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       81.73        11.80        15.52        24.13         0.76        17.59 

$`19Q LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H1 
       53.39        63.75        83.24        41.79        80.28        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       56.91        41.33        47.74        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       20.81        14.99         1.18         8.55        13.02         8.61 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        11.97        11.08         1.51 
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        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 
       18.48        44.81        13.45        36.66         0.66         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.19         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-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       18.35        13.64        21.14        27.19        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 
       90.28        30.97        30.15        26.83        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       76.41        55.40        12.53        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX 
       61.68        13.64        14.20        51.35        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       34.49         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.15        20.98        18.61        19.99         4.64        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       23.74        18.90        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS 
       25.78        50.33        35.08        79.07        89.69        59.93 
TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       72.39        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41        13.35         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       20.61        19.59         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        60.89        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       51.06        53.79        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
        5.98         1.84        11.24         8.55         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        11.84        13.38        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        0.62        10.85        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB 
        3.09        21.04        19.33        19.04        15.39        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       16.44         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       11.34         0.99        12.99        24.85        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            120.82             114.35 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            21.370             19.165 
[1] "0.1 - 120.8 (21.4)" "0.0 - 114.3 (19.2)"
[1] "hr=" "1"  
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED        15        7         0         10          1
  19Q LOSS WILD-TYPE     153       77         3         49          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q LOSS MUTATED            2        1         0         0
  19Q LOSS WILD-TYPE          5        2         1         2
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  15                153
  STAGE II                  7                 77
  STAGE III                 0                  3
  STAGE IIIA               10                 49
  STAGE IIIB                1                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19Q LOSS MUTATED      17   8  11   2
  19Q LOSS WILD-TYPE   162  83  62  10
D76V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1               17                162
  T2                   8                 83
  T3                  11                 62
  T4                   2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    28   1
  19Q LOSS WILD-TYPE 221   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     28    1
  19Q LOSS WILD-TYPE  221    2
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               28                221
  1                1                  2
[1] 2 2
[1] FALSE
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    33   0
  19Q LOSS WILD-TYPE 227   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     33    0
  19Q LOSS WILD-TYPE  227    4
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               33                227
  1                0                  4
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     8  30
  19Q LOSS WILD-TYPE 105 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8   30
  19Q LOSS WILD-TYPE  105  214
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                8                105
  MALE                 30                214
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19Q LOSS MUTATED                         0                       37
  19Q LOSS WILD-TYPE                       2                      311
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19Q LOSS MUTATED                                  1
  19Q LOSS WILD-TYPE                                6
D76V8, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       37                311
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    31   2   0   4
  19Q LOSS WILD-TYPE 284  13   1  15
D76V9, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               31                284
  R1                2                 13
  R2                0                  1
  RX                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0    24
  19Q LOSS WILD-TYPE                                1   132
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           2    12
  19Q LOSS WILD-TYPE                        15   161
D76V10, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          24                132
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          12                161
[1] 4 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
  19Q LOSS MUTATED     2  35
  19Q LOSS WILD-TYPE   9 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   35
  19Q LOSS WILD-TYPE    9  294
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               35                294
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    14   7
  20P LOSS WILD-TYPE 211 102
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                21                313 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                102 
$`20P LOSS MUTATED`
TCGA-2Y-A9H6 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5R-AA1D TCGA-BC-A10Z TCGA-CC-A3MC 
       11.74        13.02        10.78        11.08         1.12         0.13 
TCGA-DD-A113 TCGA-DD-A1EK TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A4NO 
       79.73        18.35         5.62        17.59       102.74        73.81 
TCGA-DD-A4NQ TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADM 
       12.26        59.31         5.59        44.22        40.54         0.39 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-MR-A8JO 
       13.35         0.20        10.85 

$`20P LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       47.74        18.25        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM 
        8.55         8.61        10.59         0.66        11.97         1.51 
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        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       12.72        18.48        44.81        13.45        36.66         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.19         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.07         0.10        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        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       12.95        45.11        49.15         6.02        33.04        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        27.19        55.69        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       70.06        20.12       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        90.28        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR 
       30.51        39.78        56.25        29.56       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT 
       58.16        42.81        61.68        13.64        14.20        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       51.52        50.33        46.82        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB 
       18.54        21.63        42.58        22.09        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49        20.91        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       14.33        66.67        15.58        18.21        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        21.17        21.83        23.74        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       25.08        16.37        23.64        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.41         1.84        18.74        19.99        20.61        19.59 
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        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        81.73         0.39        13.68        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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        11.24         8.55        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        11.84        13.38        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
        0.62        58.88        19.92        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
        0.76        17.59        19.76        16.44         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        7.04        10.75        10.32        11.34         0.99        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        13.55        35.77        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.13               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            102.74             120.82 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             12.26              19.76 
[1] "0.1 - 102.7 (12.3)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P LOSS MUTATED         9        7         1          5          1
  20P LOSS WILD-TYPE     159       77         2         54          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P LOSS MUTATED            0        0         0         1
  20P LOSS WILD-TYPE          7        3         1         1
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   9                159
  STAGE II                  7                 77
  STAGE III                 1                  2
  STAGE IIIA                5                 54
  STAGE IIIB                1                  7
  STAGE IIIC                0                  7
  STAGE IV                  0                  3
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20P LOSS MUTATED       9   7   7   1
  20P LOSS WILD-TYPE   170  84  66  11
D77V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                9                170
  T2                   7                 84
  T3                   7                 66
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    21   0
  20P LOSS WILD-TYPE 228   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     21    0
  20P LOSS WILD-TYPE  228    3
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               21                228
  1                0                  3
[1] 2 2
[1] FALSE
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    19   1
  20P LOSS WILD-TYPE 241   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     19    1
  20P LOSS WILD-TYPE  241    3
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               19                241
  1                1                  3
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     8  16
  20P LOSS WILD-TYPE 105 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8   16
  20P LOSS WILD-TYPE  105  228
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                8                105
  MALE                 16                228
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20P LOSS MUTATED                         1                       22
  20P LOSS WILD-TYPE                       1                      326
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20P LOSS MUTATED                                  1
  20P LOSS WILD-TYPE                                6
D77V8, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       22                326
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    22   0   0   2
  20P LOSS WILD-TYPE 293  15   1  17
D77V9, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               22                293
  R1                0                 15
  R2                0                  1
  RX                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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    13
  20P LOSS WILD-TYPE                                1   143
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           1    10
  20P LOSS WILD-TYPE                        16   163
D77V10, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          13                143
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                          10                163
[1] 4 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
  20P LOSS MUTATED     1  22
  20P LOSS WILD-TYPE  10 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   22
  20P LOSS WILD-TYPE   10  307
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               22                307
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     8   3
  20Q LOSS WILD-TYPE 217 106
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                11                323 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                106 
$`20Q LOSS MUTATED`
TCGA-2Y-A9H6 TCGA-3K-AAZ8 TCGA-5R-AA1D TCGA-DD-A113 TCGA-DD-A39Y TCGA-DD-A3A5 
       11.74        13.02        11.08        79.73         5.62       102.74 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-AAD5 TCGA-ED-A8O5 TCGA-MR-A8JO 
       73.81        12.26        44.22        13.35        10.85 

$`20Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       47.74        18.25        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55         8.61        10.78        10.59         0.66        11.97 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        1.51        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       69.57         5.03        44.42        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       17.98        14.60        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       36.66         0.66         0.07         2.86         3.19         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        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       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        90.28        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        21.63        42.58        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       18.21        18.87        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       20.98        18.61        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       23.74        18.90        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        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         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        14.04        13.15        13.41         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       81.73         0.39        13.68        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        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
        8.55        11.80         9.70         9.17         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83         3.72         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71         0.62        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       19.92        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.04        15.39        15.52        24.13         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       19.76        16.44         1.71        15.98         7.04        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
       10.32        11.34         0.99        12.99        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        40.80        79.30        11.21 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              5.62               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            102.74             120.82 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             13.02              19.33 
[1] "5.6 - 102.7 (13.0)" "0.0 - 120.8 (19.3)"
[1] "hr=" "1.5"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q LOSS MUTATED         5        3         1          2          1
  20Q LOSS WILD-TYPE     163       81         2         57          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q LOSS MUTATED            0        0         0         0
  20Q LOSS WILD-TYPE          7        3         1         2
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   5                163
  STAGE II                  3                 81
  STAGE III                 1                  2
  STAGE IIIA                2                 57
  STAGE IIIB                1                  7
  STAGE IIIC                0                  7
  STAGE IV                  0                  3
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20Q LOSS MUTATED       5   3   4   0
  20Q LOSS WILD-TYPE   174  88  69  12
D78V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                5                174
  T2                   3                 88
  T3                   4                 69
  T4                   0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     9   0
  20Q LOSS WILD-TYPE 240   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      9    0
  20Q LOSS WILD-TYPE  240    3
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                9                240
  1                0                  3
[1] 2 2
[1] FALSE
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     9   0
  20Q LOSS WILD-TYPE 251   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      9    0
  20Q LOSS WILD-TYPE  251    4
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                9                251
  1                0                  4
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   7
  20Q LOSS WILD-TYPE 108 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    7
  20Q LOSS WILD-TYPE  108  237
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                5                108
  MALE                  7                237
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20Q LOSS MUTATED                         1                       11
  20Q LOSS WILD-TYPE                       1                      337
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20Q LOSS MUTATED                                  0
  20Q LOSS WILD-TYPE                                7
D78V8, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       11                337
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of 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    10   0   0   2
  20Q LOSS WILD-TYPE 305  15   1  17
D78V9, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               10                305
  R1                0                 15
  R2                0                  1
  RX                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     4
  20Q LOSS WILD-TYPE                                1   152
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           1     7
  20Q LOSS WILD-TYPE                        16   166
D78V10, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                152
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           7                166
[1] 4 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
  20Q LOSS MUTATED     1  10
  20Q LOSS WILD-TYPE  10 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   10
  20Q LOSS WILD-TYPE   10  319
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               10                319
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    59  38
  21Q LOSS WILD-TYPE 166  71
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                97                237 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                38                 71 
$`21Q LOSS MUTATED`
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9HB TCGA-5C-A9VH 
       80.28        24.89        41.33        18.25         8.55        10.59 
TCGA-5R-AA1C TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A69H TCGA-BD-A3EP 
       11.97        27.52         5.03        44.42        14.60        13.45 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1E9 
        3.39         3.32         0.10         7.33         2.60        90.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        45.11        49.15        33.04        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB 
        5.62        25.81         7.66        13.78        30.61        32.52 
TCGA-DD-A4NI TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACE 
       26.83       114.35        13.48         0.53        12.53        63.48 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACU 
       15.42        53.19         0.30        42.81        13.64        51.52 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC 
       47.67         5.62        21.63        22.09        40.08        13.97 
TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       40.47        20.91        29.52        15.06        14.33        66.67 
TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAE8 TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAVS 
       18.25        18.61        21.83        16.37        23.64        59.93 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ 
       49.48        53.69        13.41         9.73         0.20         0.20 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A496 
        0.62         9.96        11.93        60.89        23.97         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25Z TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV2 
       81.73        13.68        21.53         1.84        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-AAU7 
        9.17         0.89         2.14        37.91        17.06         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MR-A8JO TCGA-RC-A7SF 
        2.14        13.38        12.72        16.67        10.85        19.04 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV 
       24.13         0.76         7.04        12.99        13.55        35.77 
TCGA-ZP-A9D1 
        0.69 

$`21Q LOSS WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GZ 
       23.80        53.39        63.75        83.24        41.79        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
      120.82        40.41        56.91        47.74        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG 
       20.81        14.99         1.18        13.02         8.61        10.78 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        11.08         1.51        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12        69.57        13.84         0.26        22.36        17.98 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       12.72        18.48        44.81        36.66         0.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        2.86         3.19         4.24         0.10         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B 
       79.73        37.78        83.57        53.33       113.00         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-A1EI TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       11.47         6.02        18.35        27.19        55.69        19.76 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 
       70.06        17.59        20.12       102.74       107.11         0.36 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        90.28        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
        1.45        35.67        11.41        75.65        76.41        55.40 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO 
       12.00         6.41        69.11         3.52        58.16        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.35        50.33        46.82         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADB 
        4.50        18.54        42.58        44.22        40.54        40.83 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
        0.39        14.89        15.58        18.21        18.87        19.30 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        18.15        20.98        19.99         4.64        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        18.90        15.72        25.08        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW 
       35.08        79.07        89.69        82.62        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A4XI 
       56.48        64.77        62.47        66.25        65.39        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       15.85        13.91        13.35        12.82        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 
       20.61        19.59        22.85        14.40        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
        8.12         6.38        12.03         0.03         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
       53.79        28.27        30.74        58.49        14.86        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       20.42        17.10         7.76        12.03         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.55         8.75         3.02         1.02         2.20         2.99 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       20.75        16.83        11.84        24.36        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 
        9.57        18.38        12.85        20.71         0.62        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       19.92        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        17.59        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 
       15.98        10.75        10.32        11.34         0.99        24.85 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.10               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            114.35             120.82 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             14.60              19.99 
[1] "0.1 - 114.3 (14.6)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.6"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED        50       22         1         17          2
  21Q LOSS WILD-TYPE     118       62         2         42          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q LOSS MUTATED            4        2         1         1
  21Q LOSS WILD-TYPE          3        1         0         1
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  50                118
  STAGE II                 22                 62
  STAGE III                 1                  2
  STAGE IIIA               17                 42
  STAGE IIIB                2                  6
  STAGE IIIC                4                  3
  STAGE IV                  2                  1
  STAGE IVA                 1                  0
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  21Q LOSS MUTATED      55  24  22   4
  21Q LOSS WILD-TYPE   124  67  51   8
D79V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               55                124
  T2                  24                 67
  T3                  22                 51
  T4                   4                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    74   2
  21Q LOSS WILD-TYPE 175   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     74    2
  21Q LOSS WILD-TYPE  175    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               74                175
  1                2                  1
[1] 2 2
[1] FALSE
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    82   3
  21Q LOSS WILD-TYPE 178   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     82    3
  21Q LOSS WILD-TYPE  178    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               82                178
  1                3                  1
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    27  79
  21Q LOSS WILD-TYPE  86 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     27   79
  21Q LOSS WILD-TYPE   86  165
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               27                 86
  MALE                 79                165
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  21Q LOSS MUTATED                         2                      102
  21Q LOSS WILD-TYPE                       0                      246
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  21Q LOSS MUTATED                                  2
  21Q LOSS WILD-TYPE                                5
D79V8, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                      102                246
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED    92   4   1   5
  21Q LOSS WILD-TYPE 223  11   0  14
D79V9, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               92                223
  R1                4                 11
  R2                1                  0
  RX                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0    49
  21Q LOSS WILD-TYPE                                1   107
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           6    47
  21Q LOSS WILD-TYPE                        11   126
D79V10, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          49                107
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          47                126
[1] 4 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
  21Q LOSS MUTATED     4  95
  21Q LOSS WILD-TYPE   7 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4   95
  21Q LOSS WILD-TYPE    7  234
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               95                234
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    38  20
  22Q LOSS WILD-TYPE 187  89
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                276 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                20                 89 
$`22Q LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9H0 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-5C-A9VG TCGA-5R-AA1D 
       23.80       120.82        41.33        47.74        10.78        11.08 
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A8YO 
       37.32        27.52        13.84         0.26        17.98        18.48 
TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-A1HT TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A 
       13.45         2.86         3.32        79.73        37.78         2.60 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NJ 
       55.69         5.62       107.11        32.52        26.83        30.51 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACZ TCGA-DD-AADF 
       73.81       108.76         9.30         0.53         5.62         3.78 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-ED-A459 TCGA-ED-A66Y 
       14.33        15.58        18.61        16.37        13.41         9.73 
TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB TCGA-FV-A4ZP TCGA-G3-A25S 
        0.20        14.04        13.15        19.59        81.73        13.68 
TCGA-G3-A25T TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-G3-AAV3 TCGA-K7-A5RG TCGA-K7-AAU7 
       51.06        25.25         1.84         9.17        17.06         3.72 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-QA-A7B7 
       11.84        13.38        18.38        20.71        10.85         3.09 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-WQ-AB4B 
       24.13         0.76        16.44        12.99 

$`22Q LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       27.88        40.41        56.91        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       20.81        14.99         1.18         8.55        13.02         8.61 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
       10.59         0.66        11.97         1.51        48.99        27.91 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        69.57         5.03        44.42        22.36        14.60 
TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 
       12.72        44.81        36.66         0.66         0.07         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         0.10         0.07         0.10         0.13 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         7.33         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        27.19        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       102.74        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        30.61        33.14        90.28        30.97        30.15 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      114.35        13.48        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       13.97        40.47        39.52        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        18.21        18.87        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.15        20.98        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH 
       23.74        18.90        15.72        25.08        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        49.48        53.69        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       13.35        12.82         0.20        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        20.61         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38        12.03         0.03         0.33 
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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 
       11.24         8.55        11.80         9.70         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       20.75        16.83         2.14        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-NI-A4U2 
       12.03         9.57        16.67        12.85         0.62        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       19.92        17.69        21.01        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       15.39        15.52        17.59        19.76         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 
        7.04        10.75        10.32        11.34         0.99        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       13.55        35.77        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        40.80        79.30        11.21 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.20               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            120.82             114.35 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            14.955             19.990 
[1] "0.2 - 120.8 (15.0)" "0.0 - 114.3 (20.0)"
[1] "hr=" "1.1"
D80V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED        23       21         0         13          1
  22Q LOSS WILD-TYPE     145       63         3         46          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q LOSS MUTATED            2        2         0         0
  22Q LOSS WILD-TYPE          5        1         1         2
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  23                145
  STAGE II                 21                 63
  STAGE III                 0                  3
  STAGE IIIA               13                 46
  STAGE IIIB                1                  7
  STAGE IIIC                2                  5
  STAGE IV                  2                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  22Q LOSS MUTATED      24  25  14   3
  22Q LOSS WILD-TYPE   155  66  59   9
D80V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1               24                155
  T2                  25                 66
  T3                  14                 59
  T4                   3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    43   0
  22Q LOSS WILD-TYPE 206   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     43    0
  22Q LOSS WILD-TYPE  206    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               43                206
  1                0                  3
[1] 2 2
[1] FALSE
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    50   1
  22Q LOSS WILD-TYPE 210   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     50    1
  22Q LOSS WILD-TYPE  210    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               50                210
  1                1                  3
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    24  42
  22Q LOSS WILD-TYPE  89 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     24   42
  22Q LOSS WILD-TYPE   89  202
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               24                 89
  MALE                 42                202
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  22Q LOSS MUTATED                         2                       62
  22Q LOSS WILD-TYPE                       0                      286
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  22Q LOSS MUTATED                                  2
  22Q LOSS WILD-TYPE                                5
D80V8, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       62                286
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    52   5   0   8
  22Q LOSS WILD-TYPE 263  10   1  11
D80V9, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               52                263
  R1                5                 10
  R2                0                  1
  RX                8                 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
  22Q LOSS MUTATED                                  0    22
  22Q LOSS WILD-TYPE                                1   134
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           8    36
  22Q LOSS WILD-TYPE                         9   137
D80V10, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          22                134
  BLACK OR AFRICAN AMERICAN                       8                  9
  WHITE                                          36                137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V11, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     5  56
  22Q LOSS WILD-TYPE   6 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5   56
  22Q LOSS WILD-TYPE    6  273
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  6
  NOT HISPANIC OR LATINO               56                273
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    64  19
  XP LOSS WILD-TYPE 161  90
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               83               251 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               19                90 
$`XP LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H6 
       23.80        53.39        63.75        56.91        47.74        11.74 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69I 
        0.66        11.97         5.03        13.84        17.98        12.72 
TCGA-BW-A5NO TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A 
        0.66         0.07        37.78        83.57        53.33         2.60 
TCGA-DD-A11B TCGA-DD-A39V TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NO TCGA-DD-A73B 
        0.46        21.14        33.14        30.97        73.81         9.30 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACS TCGA-DD-AACU 
       15.42        53.19        42.81        61.68        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC 
       50.33        46.82        47.67        44.22        40.08        13.97 
TCGA-DD-AADL TCGA-DD-AADP TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 
       20.91        15.06        18.87        19.30        18.25        20.98 
TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVU 
       21.83        25.08        25.78        79.07        89.69        72.39 
TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A97K TCGA-ES-A2HS 
       65.39        13.41         0.20         0.20         0.20        22.85 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A6UC 
       19.10        27.88         0.33        13.68        53.79         7.76 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-HP-A5N0 
        8.55         9.70         9.17         0.89         3.02        37.91 
TCGA-K7-A6G5 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MI-A75E TCGA-MI-A75G TCGA-QA-A7B7 
       16.83        13.38        13.97        16.67        18.38         3.09 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MF 
       19.33        15.39        15.52         0.76        16.44         7.04 
TCGA-ZP-A9CV TCGA-ZP-A9D2 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.77        24.43        40.80        79.30        11.21 

$`XP LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       83.24        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       40.41        41.33        18.25        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       11.08         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        69.57        44.42         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 
       18.48        44.81        13.45        36.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
        3.19         3.39         4.24         3.32         0.10         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D 
        0.13        79.73       113.00         7.33        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        11.47 
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        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        27.19        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-A4NH 
       13.78         0.36        30.61        32.52        90.28        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       26.83        30.51        39.78        56.25        29.56       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       12.26         0.30        80.75        78.84        23.93        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       12.00         6.41        69.11         0.30         3.52        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       13.64        14.20        51.35         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB 
       18.54        21.63        42.58        22.09        40.54        40.83 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR 
       34.49         0.39        29.52        14.89        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 
       15.58        18.21        18.25        18.15        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE 
        4.64        21.17        23.74        18.90        15.72        16.37 
TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       23.64        50.33        35.08        82.62        59.93        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        64.77        62.47        66.25        49.48        53.69 
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         9.73        12.82 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J 
       14.04        13.15        13.41        13.35         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        20.61        19.59         0.62         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        60.89        23.97         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.03        81.73         0.39        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        25.25        22.95        20.42        17.10 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV5 
       12.03         5.98         1.84        11.24        11.80         8.75 
TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A5RG 
        2.14         1.02         2.20         2.99        20.75        17.06 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD 
        3.72         2.14        11.84        24.36        12.72        12.03 
TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        12.85        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RG-A7D4 
       19.92        17.69        21.01        21.04        19.04        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V 
       17.59        19.76         1.71        15.98        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CY 
       11.34         0.99        12.99        24.85        13.55        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        12.99        45.57 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.07              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            89.69            120.82 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            19.10             19.53 
[1] "0.1 - 89.7 (19.1)"  "0.0 - 120.8 (19.5)"
[1] "hr=" "1.5"
D81V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XP LOSS MUTATED        44       24         0         13          2          2
  XP LOSS WILD-TYPE     124       60         3         46          6          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XP LOSS MUTATED          2         0         0
  XP LOSS WILD-TYPE        1         1         2
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 44               124
  STAGE II                24                60
  STAGE III                0                 3
  STAGE IIIA              13                46
  STAGE IIIB               2                 6
  STAGE IIIC               2                 5
  STAGE IV                 2                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XP LOSS MUTATED      46  28  15   2
  XP LOSS WILD-TYPE   133  63  58  10
D81V4, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1              46               133
  T2                 28                63
  T3                 15                58
  T4                  2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    65   1
  XP LOSS WILD-TYPE 184   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     65    1
  XP LOSS WILD-TYPE  184    2
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              65               184
  1               1                 2
[1] 2 2
[1] FALSE
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    72   1
  XP LOSS WILD-TYPE 188   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     72    1
  XP LOSS WILD-TYPE  188    3
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              72               188
  1               1                 3
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    18  74
  XP LOSS WILD-TYPE  95 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     18   74
  XP LOSS WILD-TYPE   95  170
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              18                95
  MALE                74               170
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XP LOSS MUTATED                         0                       89
  XP LOSS WILD-TYPE                       2                      259
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XP LOSS MUTATED                                  3
  XP LOSS WILD-TYPE                                4
D81V8, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      89               259
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    82   2   0   8
  XP LOSS WILD-TYPE 233  13   1  11
D81V9, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              82               233
  R1               2                13
  R2               0                 1
  RX               8                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
  XP LOSS MUTATED                                  0    46
  XP LOSS WILD-TYPE                                1   110
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                           5    40
  XP LOSS WILD-TYPE                        12   133
D81V10, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         46               110
  BLACK OR AFRICAN AMERICAN                      5                12
  WHITE                                         40               133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V11, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     3  84
  XP LOSS WILD-TYPE   8 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3   84
  XP LOSS WILD-TYPE    8  245
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              84               245
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    47  16
  XQ LOSS WILD-TYPE 178  93
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               63               271 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16                93 
$`XQ LOSS MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9H6 TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A112 
       23.80        63.75        11.74         0.66        10.13         5.03 
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
       13.84        17.98         0.07        37.78        83.57        53.33 
TCGA-DD-A11B TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-AACG TCGA-DD-AACI 
        0.46        33.14        73.81         9.30        15.42        53.19 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY 
       42.81        61.68        51.52        50.33        46.82        47.67 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADL TCGA-DD-AADP TCGA-DD-AADV 
       44.22        40.08        13.97        20.91        15.06        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEH 
       19.30        18.25        20.98        21.83        25.08        25.78 
TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A97K TCGA-FV-A2QR 
       72.39        13.41         0.20         0.20         0.20        19.10 
TCGA-FV-A3I0 TCGA-G3-A6UC TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV7 
       27.88         7.76         8.55         9.70         0.89         3.02 
TCGA-HP-A5N0 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MI-A75E TCGA-QA-A7B7 TCGA-RC-A7SB 
       37.91        13.38        13.97        16.67         3.09        19.33 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MF TCGA-ZP-A9CV 
       15.39        15.52         0.76        16.44         7.04        35.77 
TCGA-ZP-A9D2 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       24.43        40.80        79.30 

$`XQ LOSS WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        83.24        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        41.33        47.74        18.25 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       37.25        20.81        14.99         1.18         8.55        13.02 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
        8.61        10.78        10.59        11.97        11.08         1.51 
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-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
        0.26        22.36        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.45        36.66         0.66         0.07         2.86         3.19 
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        11.47 
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        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        30.61        32.52        90.28 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       23.93        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       12.53        63.48        12.00         6.41        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
        3.52        58.16        13.64        14.20        59.31        51.35 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       22.09        40.54        40.83        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN 
       37.64        35.67        35.05        34.49         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE0 
       14.89        14.33        66.67        15.58        18.21        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 
       18.15        18.61        19.99         4.64        21.17        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAEK 
       18.90        15.72        16.37        23.64        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       79.07        89.69        82.62        59.93        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
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         9.73        12.82 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J 
       14.04        13.15        13.41        13.35         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        20.61        19.59         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R2 
       22.85        14.40        60.89        23.97         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
       12.03         0.03         0.33        81.73         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       51.06        53.79        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 
       25.25        22.95        20.42        17.10        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 
        1.84        11.24        11.80         9.17         8.75         2.14 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD 
        3.72         2.14        11.84        24.36        12.72        12.03 
TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF 
       58.88        19.92        17.69        21.01        21.04        19.04 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       24.13        17.59        19.76         1.71        15.98        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
       10.32        11.34         0.99        12.99        24.85        13.55 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57         0.69        12.99        45.57 
TCGA-ZS-A9CG 
       11.21 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            83.57            120.82 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            18.87             19.59 
[1] "0.1 - 83.6 (18.9)"  "0.0 - 120.8 (19.6)"
[1] "hr=" "1.2"
D82V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ LOSS MUTATED        30       19         0          9          1          2
  XQ LOSS WILD-TYPE     138       65         3         50          7          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ LOSS MUTATED          1         0         0
  XQ LOSS WILD-TYPE        2         1         2
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 30               138
  STAGE II                19                65
  STAGE III                0                 3
  STAGE IIIA               9                50
  STAGE IIIB               1                 7
  STAGE IIIC               2                 5
  STAGE IV                 1                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XQ LOSS MUTATED      32  22  12   1
  XQ LOSS WILD-TYPE   147  69  61  11
D82V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1              32               147
  T2                 22                69
  T3                 12                61
  T4                  1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    46   1
  XQ LOSS WILD-TYPE 203   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     46    1
  XQ LOSS WILD-TYPE  203    2
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              46               203
  1               1                 2
[1] 2 2
[1] FALSE
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    55   0
  XQ LOSS WILD-TYPE 205   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     55    0
  XQ LOSS WILD-TYPE  205    4
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              55               205
  1               0                 4
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    14  54
  XQ LOSS WILD-TYPE  99 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     14   54
  XQ LOSS WILD-TYPE   99  190
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              14                99
  MALE                54               190
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XQ LOSS MUTATED                         0                       65
  XQ LOSS WILD-TYPE                       2                      283
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XQ LOSS MUTATED                                  3
  XQ LOSS WILD-TYPE                                4
D82V8, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      65               283
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    63   1   0   4
  XQ LOSS WILD-TYPE 252  14   1  15
D82V9, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              63               252
  R1               1                14
  R2               0                 1
  RX               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0    38
  XQ LOSS WILD-TYPE                                1   118
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           2    27
  XQ LOSS WILD-TYPE                        15   146
D82V10, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         38               118
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         27               146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V11, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  62
  XQ LOSS WILD-TYPE   9 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   62
  XQ LOSS WILD-TYPE    9  267
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              62               267
[1] 2 2
[1] FALSE
