[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/19775332/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/19782291/transformed.cor.cli.txt"

nPatients in clinical file=368, in cluster file=370, common to both=362
[1]  82 362
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               56               306 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               56               306 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              220               142 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              220               142 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               44               318 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               44               318 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               40               322 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               40               322 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               35               327 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               35               327 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               38               324 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               38               324 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               26               336 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               26               336 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               355 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               355 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              135               227 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              135               227 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              107               255 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              107               255 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              114               248 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              114               248 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               64               298 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               64               298 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              109               253 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              109               253 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              109               253 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              109               253 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               78               284 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               78               284 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              185               177 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              185               177 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19               343 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19               343 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               21               341 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               21               341 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                61                301 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                61                301 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                37                325 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                37                325 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                345 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                345 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                18                344 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                18                344 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                40                322 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                40                322 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                46                316 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                46                316 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                23                339 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                23                339 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                23                339 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                23                339 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                329 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                329 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                29                333 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                29                333 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                15                347 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                15                347 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                30                332 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                30                332 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                93                269 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                93                269 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                35                327 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                35                327 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                27                335 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                27                335 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                54                308 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                54                308 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                70                292 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                70                292 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               107                255 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               107                255 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               111                251 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               111                251 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                336 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                336 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                48                314 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                48                314 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               41               321 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               41               321 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               63               299 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               63               299 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               81               281 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               81               281 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               340 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               340 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               31               331 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               31               331 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               36               326 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               36               326 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               50               312 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               50               312 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               38               324 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               38               324 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              106               256 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              106               256 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              146               216 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              146               216 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28               334 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28               334 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               39               323 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               39               323 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               27               335 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               27               335 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               91               271 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               91               271 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               16               346 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               16               346 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               21               341 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               21               341 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              186               176 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              186               176 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               42               320 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               42               320 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              115               247 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              115               247 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              105               257 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              105               257 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                44                318 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                44                318 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                74                288 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                74                288 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                61                301 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                61                301 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                70                292 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                70                292 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                61                301 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                61                301 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                33                329 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                33                329 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               118                244 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               118                244 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               106                256 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               106                256 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                65                297 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                65                297 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               109                253 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               109                253 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               144                218 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               144                218 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               179                183 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               179                183 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                37                325 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                37                325 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                72                290 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                72                290 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                77                285 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                77                285 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                54                308 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                54                308 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                38                324 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                38                324 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                338 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                338 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                12                350 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                12                350 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               108                254 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               108                254 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                66                296 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                66                296 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               92               270 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               92               270 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               68               294 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               68               294 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 362 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=122,	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=231,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'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 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 362 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"    "PATHOLOGIC_STAGE"  "PATHOLOGY_T_STAGE"
 [4] "PATHOLOGY_N_STAGE" "PATHOLOGY_M_STAGE" "GENDER"           
 [7] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"   
[10] "RACE"              "ETHNICITY"        
YEARS_TO_BIRTH, nv=62, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
  1 181  92  74  12 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
  182    92    74    12 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1 181  92  74  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
  182    92    74    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
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, 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    34  20
  1P GAIN WILD-TYPE 195 109
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               304 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               20               109 
$`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-CC-A5UC TCGA-CC-A5UE 
        2.99        44.42         0.66         3.39        11.41         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IK TCGA-CC-A8HU TCGA-DD-A114 TCGA-DD-A11A 
        7.13        21.34         8.61        11.31        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-AAVV TCGA-DD-AAVW TCGA-DD-AAW1 
       66.67        21.17        21.83        80.71        76.18        65.39 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A26S 
       29.92        26.93         0.20        14.04         1.84        19.99 
TCGA-G3-A25W TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 
       30.74        25.25        22.95        20.78         1.84        11.80 
TCGA-G3-AAV3 TCGA-GJ-A3OU TCGA-KR-A7K7 TCGA-RC-A7SH TCGA-UB-A7MF TCGA-UB-AA0U 
       13.55        22.92        31.27        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        49.84        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       38.40        20.81        22.92         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        17.10        14.76         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 
       23.38         1.12        69.57         5.03        45.93         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         4.24         2.86         3.19         4.24 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.35         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL 
        9.99         9.83        12.00        13.12        12.56         9.14 
TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 
        4.60         9.17         6.94         8.15        79.73        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-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        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-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.15        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-AACK TCGA-DD-AACM 
       12.00        15.42         6.41        53.19         0.30        58.16 
TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       42.81        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-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       18.54        42.58        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-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       34.49         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-AAE9 
       18.15        20.98        18.61        19.99         4.64        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        26.63        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-AAW2 
       72.39        56.48        64.77        62.47        66.25        49.48 
TCGA-DD-AAW3 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       53.69        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
       12.82        13.15        13.41        13.35         0.20        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-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-A25X TCGA-G3-A25Y 
       13.68        51.06        53.79        28.27        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        22.06        14.70        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       15.78        15.65        12.23         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       11.87         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 
       17.06        16.83        11.80         2.14        21.60        29.79 
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        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       24.56        20.71         7.53        10.85        58.88        26.27 
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-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.52        36.10         0.76        17.59        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.32        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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        35.87         0.69        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       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 
            80.71            120.82 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           21.730            19.165 
[1] "0.2 - 80.7 (21.7)"  "0.0 - 120.8 (19.2)"
[1] "hr=" "1.1"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P GAIN MUTATED        22       14         0         12          3          2
  1P GAIN WILD-TYPE     149       71         3         48          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                 22               149
  STAGE II                14                71
  STAGE III                0                 3
  STAGE IIIA              12                48
  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      22  16  14   4
  1P GAIN WILD-TYPE   160  76  60   8
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1              22               160
  T2                 16                76
  T3                 14                60
  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    38   0
  1P GAIN WILD-TYPE 212   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     38    0
  1P GAIN WILD-TYPE  212    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              38               212
  1               0                 3
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    42   0
  1P GAIN WILD-TYPE 219   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     42    0
  1P GAIN WILD-TYPE  219    4
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              42               219
  1               0                 4
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    13  43
  1P GAIN WILD-TYPE 102 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     13   43
  1P GAIN WILD-TYPE  102  204
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              13               102
  MALE                43               204
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    52   1
  1P GAIN WILD-TYPE 284   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     52    1
  1P GAIN WILD-TYPE  284    6
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               52               284
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1P GAIN MUTATED                         0                       55
  1P GAIN WILD-TYPE                       2                      298
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1P GAIN MUTATED                                  1
  1P GAIN WILD-TYPE                                6
D1V9, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      55               298
  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    46   5   0   3
  1P GAIN WILD-TYPE 272  10   1  18
D1V10, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              46               272
  R1               5                10
  R2               0                 1
  RX               3                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
  1P GAIN MUTATED                                  0    33
  1P GAIN WILD-TYPE                                1   124
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           3    20
  1P GAIN WILD-TYPE                        14   157
D1V11, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         33               124
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         20               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"
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  54
  1P GAIN WILD-TYPE  13 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   54
  1P GAIN WILD-TYPE   13  278
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                13
  NOT HISPANIC OR LATINO              54               278
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   140  77
  1Q GAIN WILD-TYPE  89  52
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              217               141 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               77                52 
$`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 
       49.84        38.40        20.81        22.92         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        17.10        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        23.38         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-5264 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE 
        3.35         9.96        11.93        11.41         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       21.34         9.83         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 
        9.17         8.15        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        80.71        76.18        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y 
       65.39        53.69        29.92        26.93        13.35         9.73 
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-FV-A2QQ 
       19.99        20.61        19.59         0.62         9.96        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25W 
       19.10         8.12        12.03         0.03        13.68        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK 
       58.49        14.86        21.53        22.13        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV0 
       25.25        20.42        17.10        20.78         1.84        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80        12.23        13.55         8.75         2.14        11.87 
TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       22.92         2.99        37.71         2.14        21.60        31.27 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       12.72        13.97         9.57        16.67        22.95        24.56 
TCGA-MI-A75I TCGA-O8-A75V TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       20.71        17.69        15.39        15.52        36.10         0.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98         7.04        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CZ 
       12.99        20.22        18.28        22.78        35.77        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       35.87         0.69        25.15        12.99        45.57        40.80 
TCGA-ZS-A9CG 
       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        14.76         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        45.93         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         4.24         2.86         4.24         3.32         9.86 
TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A9FS 
       10.36         9.99        12.00        13.12        12.56         6.94 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       83.57        53.33         0.46        66.31        19.79        75.65 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 
        6.02        33.04        55.69         7.66        70.06        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NL 
      102.74       107.11        33.14        32.52        90.28        56.25 
TCGA-DD-A4NP TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
      108.76        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACG TCGA-DD-AACH 
        1.45        35.67        75.65        12.53        15.42         6.41 
TCGA-DD-AACK TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADB 
        0.30        50.33        46.82         5.62        22.09        40.83 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADV 
       39.52         3.78        29.52        14.33        15.58        18.87 
TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAEA TCGA-DD-AAEE 
       19.30        20.98        18.61        19.99        18.90        26.63 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAW2 TCGA-ED-A5KG 
       50.33        35.08        72.39        56.48        49.48        28.08 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A3RK 
       13.91         0.20        13.41        13.35         0.20        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A496 
       22.85        14.40        60.89        27.88         6.38         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CH 
       81.73         0.39        51.06        53.79        28.27        25.64 
TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
        5.92        22.95        22.06        14.70        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RF TCGA-K7-A5RG 
       15.78         0.89         1.02         2.20        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MR-A520 TCGA-MR-A8JO 
       16.83        11.80        29.79        12.03         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        26.27        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WX-AA46 
       19.04        17.59        19.76        10.75        10.32        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZS-A9CF 
       13.55        25.71        79.30 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           120.82            108.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            19.76             19.76 
[1] "0.0 - 120.8 (19.8)" "0.2 - 108.8 (19.8)"
[1] "hr=" "1"  
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED       101       56         2         30          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                101                70
  STAGE II                56                29
  STAGE III                2                 1
  STAGE IIIA              30                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     109  60  41   8
  1Q GAIN WILD-TYPE    73  32  33   4
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1             109                73
  T2                 60                32
  T3                 41                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   155   1
  1Q GAIN WILD-TYPE  95   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    155    1
  1Q GAIN WILD-TYPE   95    2
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             155                95
  1               1                 2
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   162   4
  1Q GAIN WILD-TYPE  99   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    162    4
  1Q GAIN WILD-TYPE   99    0
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             162                99
  1               4                 0
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    67 153
  1Q GAIN WILD-TYPE  48  94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     67  153
  1Q GAIN WILD-TYPE   48   94
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              67                48
  MALE               153                94
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   204   5
  1Q GAIN WILD-TYPE 132   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    204    5
  1Q GAIN WILD-TYPE  132    2
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              204               132
  YES               5                 2
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1Q GAIN MUTATED                         0                      217
  1Q GAIN WILD-TYPE                       2                      136
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1Q GAIN MUTATED                                  3
  1Q GAIN WILD-TYPE                                4
D2V9, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     217               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   197   8   1  11
  1Q GAIN WILD-TYPE 121   7   0  10
D2V10, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             197               121
  R1               8                 7
  R2               1                 0
  RX              11                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   104
  1Q GAIN WILD-TYPE                                0    53
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          11    98
  1Q GAIN WILD-TYPE                         6    79
D2V11, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                        104                53
  BLACK OR AFRICAN AMERICAN                     11                 6
  WHITE                                         98                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"
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     8 203
  1Q GAIN WILD-TYPE   5 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8  203
  1Q GAIN WILD-TYPE    5  129
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                 5
  NOT HISPANIC OR LATINO             203               129
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    20  22
  2P GAIN WILD-TYPE 209 107
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               42               316 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               22               107 
$`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        17.10 
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         9.86 
TCGA-CC-A7IE TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-DD-A113 TCGA-DD-A1E9 TCGA-DD-A1EG 
        7.13        12.56         8.61        79.73        90.71        45.11 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A73D 
       33.04        13.64        55.69        30.61        33.14        22.78 
TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AACZ TCGA-DD-AAD6 
        1.45        13.48        76.41        53.19         5.62        22.09 
TCGA-DD-AADO TCGA-DD-AAVW TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS 
       14.89        76.18        12.82        13.41         1.84        22.85 
TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z TCGA-LG-A6GG TCGA-UB-A7MA TCGA-YA-A8S7 
       51.06        30.74        21.53        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        49.84        47.74        11.74        38.40        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG 
       22.92         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        14.76         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        23.38         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        45.93         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-5264 
        4.24         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        3.32         9.96        10.36        11.93        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IL 
        8.94        21.34         9.83        12.00        13.12         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 
        4.60        11.31         9.17         6.94         8.15        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V 
       11.47        12.95        49.15         6.02        18.35        21.14 
TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        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-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-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       44.22        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-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        26.63 
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-AAVV TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        80.71        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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        14.04        13.15        13.35         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-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-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
       13.68        53.79        28.27        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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       20.42        17.10        22.06        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       14.14         1.84        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89         8.75         2.14        11.87        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83        11.80         2.14        21.60        31.27        29.79 
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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        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        36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV 
       12.99        20.22        24.85        18.28        22.78        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        35.87         0.69        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.45              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            90.71            120.82 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           22.435            19.560 
[1] "1.4 - 90.7 (22.4)"  "0.0 - 120.8 (19.6)"
[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     157       74         3         49          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               157
  STAGE II                11                74
  STAGE III                0                 3
  STAGE IIIA              11                49
  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   167  78  61  10
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1              15               167
  T2                 14                78
  T3                 13                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"
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    30   2
  2P GAIN WILD-TYPE 220   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     30    2
  2P GAIN WILD-TYPE  220    1
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              30               220
  1               2                 1
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    30   2
  2P GAIN WILD-TYPE 231   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     30    2
  2P GAIN WILD-TYPE  231    2
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              30               231
  1               2                 2
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    26  18
  2P GAIN WILD-TYPE  89 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     26   18
  2P GAIN WILD-TYPE   89  229
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              26                89
  MALE                18               229
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    41   0
  2P GAIN WILD-TYPE 295   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     41    0
  2P GAIN WILD-TYPE  295    7
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               41               295
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2P GAIN MUTATED                         0                       42
  2P GAIN WILD-TYPE                       2                      311
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2P GAIN MUTATED                                  2
  2P GAIN WILD-TYPE                                5
D3V9, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      42               311
  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 280  10   1  20
D3V10, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              38               280
  R1               5                10
  R2               0                 1
  RX               1                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   142
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           1    28
  2P GAIN WILD-TYPE                        16   149
D3V11, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15               142
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         28               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"
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2  42
  2P GAIN WILD-TYPE  11 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   42
  2P GAIN WILD-TYPE   11  290
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO              42               290
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    19  19
  2Q GAIN WILD-TYPE 210 110
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               38               320 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19               110 
$`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        17.10        48.99        37.32        10.13 
TCGA-CC-A7IE TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-DD-A113 TCGA-DD-A1E9 TCGA-DD-A1EJ 
        7.13        12.56         8.61        79.73        90.71        33.04 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A 
       13.64        55.69        30.61        22.78         1.45        13.48 
TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADO 
       76.41        53.19        51.52         5.62        22.09        14.89 
TCGA-DD-AADU TCGA-DD-AAVW TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS 
       18.21        76.18        12.82        13.41         1.84        22.85 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-AAV6 TCGA-LG-A6GG 
       13.68        51.06        30.74        21.53         2.14        12.72 
TCGA-UB-A7MA TCGA-YA-A8S7 
       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        49.84        47.74 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        38.40        20.81        22.92         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        14.76 
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        23.38         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 
       45.93         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         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT 
        2.86         3.19         3.39         4.24         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        9.86         9.96        10.36        11.93        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IL 
        8.94        21.34         9.83        12.00        13.12         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 
        4.60        11.31         9.17         6.94         8.15        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       11.47        12.95        45.11        49.15         6.02        18.35 
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-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-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-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 
        9.30        23.05        35.67       114.35         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-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-AACV 
       61.68        13.64        14.20        59.31        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-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-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-AADP TCGA-DD-AADQ 
       34.49        20.91         0.39        29.52        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        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        26.63 
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-AAVV TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        80.71        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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        14.04        13.15        13.35         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-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-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
       53.79        28.27        58.49        14.86        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       17.10        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        21.60        31.27        29.79        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        22.95        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        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        36.10 
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-AA44 
       10.75        10.32        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       24.85        18.28        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       35.87         0.69        25.15        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       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 
           18.230            19.775 
[1] "1.4 - 90.7 (18.2)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
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     158       74         3         50          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               158
  STAGE II                11                74
  STAGE III                0                 3
  STAGE IIIA              10                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
  2Q GAIN MUTATED      14  13  12   1
  2Q GAIN WILD-TYPE   168  79  62  11
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              14               168
  T2                 13                79
  T3                 12                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"
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    31   1
  2Q GAIN WILD-TYPE 219   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     31    1
  2Q GAIN WILD-TYPE  219    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              31               219
  1               1                 2
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    30   2
  2Q GAIN WILD-TYPE 231   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     30    2
  2Q GAIN WILD-TYPE  231    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              30               231
  1               2                 2
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    23  17
  2Q GAIN WILD-TYPE  92 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     23   17
  2Q GAIN WILD-TYPE   92  230
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              23                92
  MALE                17               230
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    37   0
  2Q GAIN WILD-TYPE 299   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     37    0
  2Q GAIN WILD-TYPE  299    7
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               37               299
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2Q GAIN MUTATED                         0                       38
  2Q GAIN WILD-TYPE                       2                      315
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2Q GAIN MUTATED                                  2
  2Q GAIN WILD-TYPE                                5
D4V9, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      38               315
  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 283  11   1  20
D4V10, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              35               283
  R1               4                11
  R2               0                 1
  RX               1                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   141
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           1    23
  2Q GAIN WILD-TYPE                        16   154
D4V11, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         16               141
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         23               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"
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2  38
  2Q GAIN WILD-TYPE  11 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   38
  2Q GAIN WILD-TYPE   11  294
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO              38               294
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    20  13
  3P GAIN WILD-TYPE 209 116
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               33               325 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13               116 
$`3P GAIN MUTATED`
TCGA-2Y-A9GS TCGA-5R-AA1C TCGA-BC-A217 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-A3M9 
       23.80        17.10        45.93        14.60         0.66         9.86 
TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-DD-A114 TCGA-DD-A11C TCGA-DD-A1EF 
        9.83        12.56         8.61        37.78        21.76        12.95 
TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-AACZ TCGA-DD-AAD6 
       33.04         5.62        78.84         1.45         5.62        22.09 
TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE6 
       40.47        20.91        29.52        66.67        18.21         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEE TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-AAV2 
       23.74        26.63         1.84        22.85         6.38        12.23 
TCGA-MI-A75G TCGA-NI-A8LF TCGA-UB-A7ME 
       22.95        26.27        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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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 
       14.76         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        23.38 
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-5264 
        4.24         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        3.32         9.96        10.36        11.93        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IL 
        8.94         7.13        21.34        12.00        13.12         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        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-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-A1EL 
       11.47        45.11        49.15         6.02        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-A73A 
       73.81       108.76        12.26         0.30        80.75        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
        9.30        23.05        22.78        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-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-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE 
       44.22        40.08        40.54        40.83        13.97        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
        3.78        37.64        35.67        35.05        34.49         0.39 
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-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG 
       21.17        21.83        18.90        15.72        25.08        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        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-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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        9.96        11.93        14.40        60.89        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-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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       22.06        14.70        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.78        15.65        11.80        13.55         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       21.60        31.27        29.79        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        24.56        20.71         7.53        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        36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        25.15        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.66              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            78.84            120.82 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            18.21             19.76 
[1] "0.7 - 78.8 (18.2)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
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     153       77         3         54          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               153
  STAGE II                 8                77
  STAGE III                0                 3
  STAGE IIIA               6                54
  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   163  82  68  12
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1              19               163
  T2                 10                82
  T3                  6                68
  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 228   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     22    1
  3P GAIN WILD-TYPE  228    2
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              22               228
  1               1                 2
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    26   1
  3P GAIN WILD-TYPE 235   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     26    1
  3P GAIN WILD-TYPE  235    3
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              26               235
  1               1                 3
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     7  28
  3P GAIN WILD-TYPE 108 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      7   28
  3P GAIN WILD-TYPE  108  219
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               7               108
  MALE                28               219
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    32   0
  3P GAIN WILD-TYPE 304   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     32    0
  3P GAIN WILD-TYPE  304    7
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               32               304
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3P GAIN MUTATED                         0                       35
  3P GAIN WILD-TYPE                       2                      318
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3P GAIN MUTATED                                  0
  3P GAIN WILD-TYPE                                7
D5V9, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      35               318
  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 287  15   1  17
D5V10, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              31               287
  R1               0                15
  R2               0                 1
  RX               4                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
  3P GAIN MUTATED                                  0    17
  3P GAIN WILD-TYPE                                1   140
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           2    16
  3P GAIN WILD-TYPE                        15   161
D5V11, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17               140
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         16               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"
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  32
  3P GAIN WILD-TYPE  11 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   32
  3P GAIN WILD-TYPE   11  300
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO              32               300
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    20  16
  3Q GAIN WILD-TYPE 209 113
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               36               322 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16               113 
$`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        17.10        10.13        45.93        14.60 
TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-DD-A114 
        0.66         9.86         9.83        12.56         8.61        37.78 
TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-A73E 
       21.76        12.95        33.04         5.62        78.84         1.45 
TCGA-DD-AACL TCGA-DD-AACZ TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR 
        3.52         5.62        40.47        20.91        29.52        66.67 
TCGA-DD-AADU TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEE TCGA-DD-AAVS TCGA-ES-A2HS 
       18.21         4.64        23.74        26.63        59.93        22.85 
TCGA-FV-A3R2 TCGA-G3-A7M9 TCGA-LG-A9QD TCGA-MI-A75G TCGA-NI-A8LF TCGA-UB-A7MD 
        6.38         1.84        12.03        22.95        26.27         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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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        14.76 
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        23.38         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         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA 
        3.19         3.39         4.24         3.35         3.32         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       21.34        12.00        13.12         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        9.17         6.94         8.15        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-AACM 
       15.42         6.41        53.19        69.11         0.30        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-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-AAVU TCGA-DD-AAVV 
       35.08        79.07        89.69        82.62        72.39        80.71 
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        29.92        26.93        28.08        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-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-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-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-A6UC TCGA-G3-A7M5 
       25.25        22.95        20.42        17.10        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89         8.75         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83        11.80         2.14        21.60        31.27 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       29.79        12.72        13.97         9.57        16.67        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       20.71         7.53        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 
       36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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        35.87         0.69        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.66              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            78.84            120.82 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            15.85             19.89 
[1] "0.7 - 78.8 (15.9)"  "0.0 - 120.8 (19.9)"
[1] "hr=" "1.7"
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     152       76         3         55          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               152
  STAGE II                 9                76
  STAGE III                0                 3
  STAGE IIIA               5                55
  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   162  81  67  12
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              20               162
  T2                 11                81
  T3                  7                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"
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    24   1
  3Q GAIN WILD-TYPE 226   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     24    1
  3Q GAIN WILD-TYPE  226    2
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              24               226
  1               1                 2
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    27   1
  3Q GAIN WILD-TYPE 234   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     27    1
  3Q GAIN WILD-TYPE  234    3
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              27               234
  1               1                 3
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     8  30
  3Q GAIN WILD-TYPE 107 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8   30
  3Q GAIN WILD-TYPE  107  217
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               8               107
  MALE                30               217
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    35   0
  3Q GAIN WILD-TYPE 301   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     35    0
  3Q GAIN WILD-TYPE  301    7
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               35               301
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3Q GAIN MUTATED                         0                       37
  3Q GAIN WILD-TYPE                       2                      316
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3Q GAIN MUTATED                                  1
  3Q GAIN WILD-TYPE                                6
D6V9, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      37               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
  3Q GAIN MUTATED    34   0   0   4
  3Q GAIN WILD-TYPE 284  15   1  17
D6V10, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              34               284
  R1               0                15
  R2               0                 1
  RX               4                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 GAIN MUTATED                                  0    17
  3Q GAIN WILD-TYPE                                1   140
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                           3    18
  3Q GAIN WILD-TYPE                        14   159
D6V11, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17               140
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         18               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"
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3  34
  3Q GAIN WILD-TYPE  10 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   34
  3Q GAIN WILD-TYPE   10  298
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                10
  NOT HISPANIC OR LATINO              34               298
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    20   6
  4P GAIN WILD-TYPE 209 123
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               26               332 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               123 
$`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-CC-A7IG TCGA-CC-A7IH TCGA-DD-A118 TCGA-DD-A11A 
        9.86        10.36         9.83        12.00       113.00         2.60 
TCGA-DD-A1EC TCGA-DD-A1EH TCGA-DD-A73G TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AADB 
       19.79        49.15       114.35        53.19        58.16        40.83 
TCGA-DD-AADO TCGA-DD-AAVS TCGA-ED-A82E TCGA-ED-A8O5 TCGA-G3-A3CG TCGA-LG-A6GG 
       14.89        59.93        13.41        13.35        22.13        12.72 
TCGA-T1-A6J8 TCGA-WQ-A9G7 
        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        49.84        47.74        18.25 
TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       38.40        22.92         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        17.10        14.76         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        23.38         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        45.93         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-5264 TCGA-CC-A1HT 
        4.24         2.86         3.39         4.24         3.35         3.32 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
        9.96        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
       21.34        13.12        12.56         8.61         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57        53.33         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       90.71        79.40        66.31        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11         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-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-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-AACJ 
       12.53        63.48        12.00        15.42         6.41        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        0.30         3.52        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-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-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        26.63 
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-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        72.39        80.71        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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-ED-A97K 
       12.82         0.20        14.04        13.15         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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       22.06        14.70        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        8.75         2.14        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        21.60        31.27        29.79        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        22.95        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        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        36.10 
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-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        10.32        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       18.28        22.78        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 
       35.87         0.69        25.15        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.76              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           114.35            120.82 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           14.150            19.875 
[1] "0.8 - 114.3 (14.2)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1.9"
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     161       78         2         55          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               161
  STAGE II                 7                78
  STAGE III                1                 2
  STAGE IIIA               5                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
  4P GAIN MUTATED      12   6   8   0
  4P GAIN WILD-TYPE   170  86  66  12
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1              12               170
  T2                  6                86
  T3                  8                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"
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    19   0
  4P GAIN WILD-TYPE 231   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     19    0
  4P GAIN WILD-TYPE  231    3
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              19               231
  1               0                 3
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    21   0
  4P GAIN WILD-TYPE 240   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     21    0
  4P GAIN WILD-TYPE  240    4
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              21               240
  1               0                 4
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    12  14
  4P GAIN WILD-TYPE 103 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     12   14
  4P GAIN WILD-TYPE  103  233
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              12               103
  MALE                14               233
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    24   0
  4P GAIN WILD-TYPE 312   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     24    0
  4P GAIN WILD-TYPE  312    7
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               24               312
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4P GAIN MUTATED                         0                       26
  4P GAIN WILD-TYPE                       2                      327
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4P GAIN MUTATED                                  0
  4P GAIN WILD-TYPE                                7
D7V9, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      26               327
  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 295  14   1  19
D7V10, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              23               295
  R1               1                14
  R2               0                 1
  RX               2                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   145
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1    13
  4P GAIN WILD-TYPE                        16   164
D7V11, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         12               145
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         13               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"
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  26
  4P GAIN WILD-TYPE  13 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   26
  4P GAIN WILD-TYPE   13  306
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                13
  NOT HISPANIC OR LATINO              26               306
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     5   2
  4Q GAIN WILD-TYPE 224 127
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               351 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               127 
$`4Q GAIN MUTATED`
TCGA-CC-5261 TCGA-CC-A7IG TCGA-DD-A1EC TCGA-DD-AACI TCGA-ED-A82E TCGA-G3-A3CG 
        3.19         9.83        19.79        53.19        13.41        22.13 
TCGA-G3-AAUZ 
       15.78 

$`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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        38.40        20.81        22.92 
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        17.10        14.76         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        23.38         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 
       45.93         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         4.24 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.39         4.24         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.96        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
        7.13        21.34        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.14         4.60        11.31         9.17         6.94         8.15 
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-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        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-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-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-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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        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        29.92        26.93        28.08 
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-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-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-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-A25W 
        0.39        13.68        51.06        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        25.25        22.95        20.42        17.10        22.06 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14         1.84        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        22.92         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83        11.80         2.14        21.60 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       31.27        29.79        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        22.95        24.56        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        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        36.10         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-AA44 
       10.75        10.32        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       24.85        18.28        22.78        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        35.87         0.69        25.15        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       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 
            15.78             19.76 
[1] "3.2 - 53.2 (15.8)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
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     168       82         3         59          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               168
  STAGE II                 3                82
  STAGE III                0                 3
  STAGE IIIA               1                59
  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   179  89  73  12
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               3               179
  T2                  3                89
  T3                  1                73
  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 243   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    0
  4Q GAIN WILD-TYPE  243    3
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               7               243
  1               0                 3
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7   0
  4Q GAIN WILD-TYPE 254   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    0
  4Q GAIN WILD-TYPE  254    4
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               7               254
  1               0                 4
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     2   5
  4Q GAIN WILD-TYPE 113 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    5
  4Q GAIN WILD-TYPE  113  242
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2               113
  MALE                 5               242
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7   0
  4Q GAIN WILD-TYPE 329   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    0
  4Q GAIN WILD-TYPE  329    7
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                7               329
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4Q GAIN MUTATED                         0                        7
  4Q GAIN WILD-TYPE                       2                      346
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4Q GAIN MUTATED                                  0
  4Q GAIN WILD-TYPE                                7
D8V9, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                       7               346
  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 313  14   1  20
D8V10, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               5               313
  R1               1                14
  R2               0                 1
  RX               1                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   153
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     2
  4Q GAIN WILD-TYPE                        17   175
D8V11, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4               153
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                          2               175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   6
  4Q GAIN WILD-TYPE  12 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    6
  4Q GAIN WILD-TYPE   12  326
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO               6               326
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    74  59
  5P GAIN WILD-TYPE 155  70
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              133               225 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               59                70 
$`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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       47.74        20.81        22.92         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        45.93 
TCGA-BC-A3KG TCGA-BD-A3EP TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MB 
       22.36        13.45         4.24         3.35         3.32        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IL 
       11.93        11.41         9.99         9.83        13.12         9.14 
TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11D 
       11.31         8.15        83.57        53.33       113.00        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V 
       90.71        79.40        66.31        11.47        12.95        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 
       55.69         5.62         7.66        17.59       102.74        13.78 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73G 
        0.36        90.28        39.78        73.81        78.84       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ 
       13.48         0.53        12.00        15.42        53.19        69.11 
TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD8 
       13.64        50.33         5.62        21.63        44.22        40.08 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU 
       13.97         3.78        29.52        14.33        66.67        18.21 
TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAEA TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK 
       18.25        18.61        18.90        26.63        23.64        35.08 
TCGA-DD-AAVV TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66X 
       80.71        64.77        66.25        49.48        29.92        13.35 
TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB 
        9.73        14.04        13.15        13.41         1.84        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 
        0.62         9.96        14.40        19.10        27.88         0.03 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG 
       81.73         0.39        51.06        30.74        58.49        22.13 
TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV5 
       25.25        17.10        14.70        11.80        12.23         8.75 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.20         2.99        21.60        29.79        12.72        13.97 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       22.95        20.71        58.88        26.27        17.69        21.01 
TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 
       19.04        36.10        15.98         7.04        10.75         0.99 
TCGA-WQ-AB4B TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       12.99        18.28        22.78        23.21         0.69        25.15 
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        38.40         8.61        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
       17.10        14.76         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        23.38         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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        3.39         9.86         9.96         8.94         7.13        21.34 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS 
       12.00        12.56         8.61         4.60         9.17         6.94 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       79.73        37.78         7.33         2.60         0.46        21.76 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
       18.35        13.64        27.19        19.76        25.81        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
       20.12       107.11        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       30.15        26.83        30.51        56.25        29.56       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-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       22.78         1.45        35.67        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL 
       55.40        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-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE 
       42.58        22.09        40.54        40.83        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-AADO TCGA-DD-AADP TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       14.89        15.06        15.58        18.87        19.30        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-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       23.74        15.72        25.08        25.78        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-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       62.47        65.39        53.69        26.93        28.08        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        12.82         0.20        13.35         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ 
       19.99        20.61        11.93        22.85        60.89        23.97 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U 
        8.12         6.38        12.03         0.33        13.68        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.23        22.95        20.42        22.06        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14         1.84        15.78        15.65        13.55         0.89 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RF 
        2.14        11.87        22.92         1.02        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A9QD 
       17.06        16.83        11.80         2.14        31.27        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-QA-A7B7 
        9.57        16.67        24.56         7.53        10.85         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA 
       21.04        19.33        15.39        15.52         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA44 
       19.76        16.44         1.71        10.32        11.34        20.22 
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        35.87        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              0.20 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           114.35            120.82 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            18.61             20.12 
[1] "0.0 - 114.3 (18.6)" "0.2 - 120.8 (20.1)"
[1] "hr=" "1.4"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P GAIN MUTATED        56       34         1         29          4          1
  5P GAIN WILD-TYPE     115       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                 56               115
  STAGE II                34                51
  STAGE III                1                 2
  STAGE IIIA              29                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      59  37  36   3
  5P GAIN WILD-TYPE   123  55  38   9
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1              59               123
  T2                 37                55
  T3                 36                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    89   0
  5P GAIN WILD-TYPE 161   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     89    0
  5P GAIN WILD-TYPE  161    3
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              89               161
  1               0                 3
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    96   1
  5P GAIN WILD-TYPE 165   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     96    1
  5P GAIN WILD-TYPE  165    3
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              96               165
  1               1                 3
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    41  94
  5P GAIN WILD-TYPE  74 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     41   94
  5P GAIN WILD-TYPE   74  153
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              41                74
  MALE                94               153
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   124   5
  5P GAIN WILD-TYPE 212   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    124    5
  5P GAIN WILD-TYPE  212    2
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO              124               212
  YES               5                 2
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5P GAIN MUTATED                         0                      132
  5P GAIN WILD-TYPE                       2                      221
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5P GAIN MUTATED                                  3
  5P GAIN WILD-TYPE                                4
D9V9, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     132               221
  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   120   6   0   6
  5P GAIN WILD-TYPE 198   9   1  15
D9V10, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0             120               198
  R1               6                 9
  R2               0                 1
  RX               6                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0    58
  5P GAIN WILD-TYPE                                1    99
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           7    63
  5P GAIN WILD-TYPE                        10   114
D9V11, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         58                99
  BLACK OR AFRICAN AMERICAN                      7                10
  WHITE                                         63               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     5 122
  5P GAIN WILD-TYPE   8 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5  122
  5P GAIN WILD-TYPE    8  210
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 8
  NOT HISPANIC OR LATINO             122               210
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    60  45
  5Q GAIN WILD-TYPE 169  84
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              105               253 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               45                84 
$`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        49.84        47.74 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Q 
       22.92         1.18         8.55        13.02        10.78        37.32 
TCGA-BC-A10W TCGA-BC-A112 TCGA-CC-5264 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        2.99         5.03         3.35        10.36        11.93        11.41 
TCGA-CC-A7IG TCGA-CC-A7IL TCGA-CC-A9FW TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11D 
        9.83         9.14         8.15        53.33       113.00        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       90.71        79.40        11.47        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-A73A TCGA-DD-A73G TCGA-DD-AA3A 
       39.78        73.81        78.84        23.93       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ 
        0.53        55.40        12.00        15.42        53.19        69.11 
TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AADC TCGA-DD-AADF 
       13.64        50.33         5.62        21.63        13.97         3.78 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE0 
        0.39        29.52        14.33        66.67        18.21        18.25 
TCGA-DD-AAE3 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVV TCGA-DD-AAVX 
       18.61        18.90        23.64        35.08        80.71        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        29.92         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-A7M5 
        0.39        51.06        30.74        22.13        17.10        14.70 
TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-LG-A6GG 
       11.80         8.75         2.20         2.99        21.60        12.72 
TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF 
       13.97        22.95        20.71        26.27        17.69        19.04 
TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CZ 
       36.10         0.99        12.99        18.28        22.78        23.21 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
        0.69        25.15        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        38.40        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        17.10        14.76         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 
       23.38         1.12        69.57        44.42        45.93         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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UD 
        3.39         4.24         3.32         9.86         9.96         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        8.94         7.13        21.34        12.00        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 
        8.61         4.60        11.31         9.17         6.94        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        26.63        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        26.93        28.08 
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-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       22.06        20.78        11.87        14.14         1.84        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       15.65        12.23        13.55         0.89         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
       22.92         1.02        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C 
       11.80         2.14        31.27        29.79        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF 
       16.67        24.56         7.53        10.85        58.88        21.01 
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-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-WX-AA44 TCGA-WX-AA46 TCGA-YA-A8S7 
       10.75        10.32        11.34        20.22        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       35.77        25.71        35.87        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.20 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           114.35            120.82 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            18.61             19.99 
[1] "0.0 - 114.3 (18.6)" "0.2 - 120.8 (20.0)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q GAIN MUTATED        47       29         1         17          3          1
  5Q GAIN WILD-TYPE     124       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                 47               124
  STAGE II                29                56
  STAGE III                1                 2
  STAGE IIIA              17                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      49  33  23   2
  5Q GAIN WILD-TYPE   133  59  51  10
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1              49               133
  T2                 33                59
  T3                 23                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    70   0
  5Q GAIN WILD-TYPE 180   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     70    0
  5Q GAIN WILD-TYPE  180    3
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              70               180
  1               0                 3
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    75   1
  5Q GAIN WILD-TYPE 186   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     75    1
  5Q GAIN WILD-TYPE  186    3
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              75               186
  1               1                 3
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    27  80
  5Q GAIN WILD-TYPE  88 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     27   80
  5Q GAIN WILD-TYPE   88  167
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              27                88
  MALE                80               167
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    97   5
  5Q GAIN WILD-TYPE 239   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     97    5
  5Q GAIN WILD-TYPE  239    2
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               97               239
  YES               5                 2
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5Q GAIN MUTATED                         0                      105
  5Q GAIN WILD-TYPE                       2                      248
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5Q GAIN MUTATED                                  2
  5Q GAIN WILD-TYPE                                5
D10V9, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     105               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
  5Q GAIN MUTATED    98   4   0   4
  5Q GAIN WILD-TYPE 220  11   1  17
D10V10, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              98               220
  R1               4                11
  R2               0                 1
  RX               4                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
  5Q GAIN MUTATED                                  0    47
  5Q GAIN WILD-TYPE                                1   110
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           6    49
  5Q GAIN WILD-TYPE                        11   128
D10V11, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         47               110
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         49               128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     5  98
  5Q GAIN WILD-TYPE   8 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5   98
  5Q GAIN WILD-TYPE    8  234
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 8
  NOT HISPANIC OR LATINO              98               234
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    69  43
  6P GAIN WILD-TYPE 160  86
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              112               246 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               43                86 
$`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        49.84        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        17.10        27.52 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       45.93        22.36        14.60        44.81        13.45         0.66 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG 
        4.24         3.35        11.93         8.94         7.13         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-DD-A114 
       12.00        13.12         8.61         9.14        11.31        37.78 
TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A8 
        7.33        45.11        49.15        55.69         5.62         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E 
       30.61        29.56        80.75         9.30        22.78         1.45 
TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
        0.53        75.65        76.41        12.53        63.48        12.00 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AAD3 
       53.19        69.11        42.81        13.64        51.35        42.58 
TCGA-DD-AADA TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ 
       40.54        37.64        20.91        29.52        14.89        14.33 
TCGA-DD-AADV TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAEK 
       18.87        18.25        18.61        23.74        25.78        35.08 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAW2 
       82.62        59.93        80.71        76.18        64.77        49.48 
TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       53.69        13.35         0.20        13.41        13.35         1.84 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S 
       19.59         0.62        22.85        27.88         6.38        13.68 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL 
       53.79        58.49        22.13        19.23        25.25        20.42 
TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-KR-A7K2 TCGA-LG-A6GG 
       22.06        11.80        13.55         0.89        21.60        12.72 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SK 
       22.95        24.56        20.71        26.27        21.04        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 
       36.10        17.59        16.44         7.04        10.75         0.99 
TCGA-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD 
       20.22        22.78        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        38.40        22.92 
TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55        10.59         0.66        14.76         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        23.38         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         4.24 
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         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IJ TCGA-CC-A8HT 
       10.36        11.41         9.99        21.34        12.56         4.60 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        9.17         6.94         8.15        79.73        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
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-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      102.74       107.11        13.78        33.14        32.52        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-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A 
       73.81       108.76        12.26         0.30        78.84        23.93 
TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC 
       23.05        35.67       114.35        13.48        11.41        55.40 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO 
       15.42         6.41         0.30         3.52        58.16        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        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-AAD5 
       47.67         5.62         4.50        18.54        21.63        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.08        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP 
        3.78        35.67        35.05        34.49         0.39        15.06 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 
       66.67        15.58        18.21        19.30        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        26.63        23.64        50.33        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       89.69        72.39        56.48        62.47        66.25        65.39 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       29.92        26.93        28.08        13.91         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       12.82        14.04        13.15         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       20.61         9.96        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.10         8.12        12.03         0.03         0.33        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39        51.06        28.27        30.74        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M5 
       25.64         5.92        19.53        22.95        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       12.23         8.75         2.14        11.87        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       11.80         2.14        31.27        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
        9.57        16.67         7.53        10.85        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-T1-A6J8 
       21.01         3.09        19.33        19.04        15.39         0.76 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
       19.76         1.71        15.98        10.32        11.34        12.99 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        18.28        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
        0.69        25.15        12.99        40.80        79.30        11.21 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.20              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            82.62            120.82 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           20.320            19.645 
[1] "0.2 - 82.6 (20.3)"  "0.0 - 120.8 (19.6)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P GAIN MUTATED        48       32         1         21          3          1
  6P GAIN WILD-TYPE     123       53         2         39          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                 48               123
  STAGE II                32                53
  STAGE III                1                 2
  STAGE IIIA              21                39
  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      49  35  26   3
  6P GAIN WILD-TYPE   133  57  48   9
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1              49               133
  T2                 35                57
  T3                 26                48
  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    78   0
  6P GAIN WILD-TYPE 172   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     78    0
  6P GAIN WILD-TYPE  172    3
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              78               172
  1               0                 3
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    83   2
  6P GAIN WILD-TYPE 178   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     83    2
  6P GAIN WILD-TYPE  178    2
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              83               178
  1               2                 2
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    32  82
  6P GAIN WILD-TYPE  83 165
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     32   82
  6P GAIN WILD-TYPE   83  165
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              32                83
  MALE                82               165
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   108   1
  6P GAIN WILD-TYPE 228   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    108    1
  6P GAIN WILD-TYPE  228    6
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO              108               228
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6P GAIN MUTATED                         0                      111
  6P GAIN WILD-TYPE                       2                      242
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6P GAIN MUTATED                                  3
  6P GAIN WILD-TYPE                                4
D11V9, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     111               242
  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   102   5   1   6
  6P GAIN WILD-TYPE 216  10   0  15
D11V10, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0             102               216
  R1               5                10
  R2               1                 0
  RX               6                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0    57
  6P GAIN WILD-TYPE                                1   100
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           7    50
  6P GAIN WILD-TYPE                        10   127
D11V11, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         57               100
  BLACK OR AFRICAN AMERICAN                      7                10
  WHITE                                         50               127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     6 105
  6P GAIN WILD-TYPE   7 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6  105
  6P GAIN WILD-TYPE    7  227
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 7
  NOT HISPANIC OR LATINO             105               227
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    38  24
  6Q GAIN WILD-TYPE 191 105
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               62               296 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               24               105 
$`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        49.84        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-5264 TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7II 
        3.35        11.93         8.94         7.13        12.00        13.12 
TCGA-CC-A7IK TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39Y 
        8.61        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-AAVV TCGA-DD-AAW2 TCGA-ED-A66X 
       18.61        25.78        35.08        80.71        49.48        13.35 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CK 
       19.59         0.62        13.68        53.79        22.13        19.23 
TCGA-G3-A5SI TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H 
       25.25        11.80        21.60        12.72        22.95        24.56 
TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MF TCGA-WX-AA44 
       21.04        15.52        36.10        16.44         7.04        20.22 
TCGA-YA-A8S7 TCGA-ZS-A9CD 
       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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD 
       20.81        22.92         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 
       17.10        14.76         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 
       23.38         1.12        69.57         5.03        44.42        45.93 
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 
        4.24         2.86         3.19         3.39         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IG 
        9.96        10.36        11.41         9.99        21.34         9.83 
TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       12.56         9.14         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        8.15        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-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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        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-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       78.84        23.93        23.05         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE 
       13.48         0.53        11.41        75.65        55.40        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        53.19         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
       58.16        61.68        13.64        14.20        59.31        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-AADP TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       15.06        66.67        15.58        18.21        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-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.83        23.74        18.90        15.72        25.08        26.63 
TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       23.64        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-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        53.69        29.92        26.93        28.08        13.91 
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-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-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       20.61         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-A25V 
        0.03         0.33        81.73         0.39        51.06        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-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 
       19.53        22.95        20.42        17.10        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89         8.75         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83        11.80         2.14        31.27        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 
       13.97        12.03         9.57        16.67        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.33        19.04        15.39         0.76        17.59        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-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY 
       12.99        24.85        18.28        22.78        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE 
       23.21        35.87         0.69        25.15        12.99        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.62              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            80.71            120.82 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            18.92             19.89 
[1] "0.6 - 80.7 (18.9)"  "0.0 - 120.8 (19.9)"
[1] "hr=" "1.3"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q GAIN MUTATED        25       17         1         13          2          1
  6Q GAIN WILD-TYPE     146       68         2         47          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                 25               146
  STAGE II                17                68
  STAGE III                1                 2
  STAGE IIIA              13                47
  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      25  19  16   3
  6Q GAIN WILD-TYPE   157  73  58   9
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1              25               157
  T2                 19                73
  T3                 16                58
  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    45   0
  6Q GAIN WILD-TYPE 205   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     45    0
  6Q GAIN WILD-TYPE  205    3
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              45               205
  1               0                 3
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    44   2
  6Q GAIN WILD-TYPE 217   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     44    2
  6Q GAIN WILD-TYPE  217    2
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              44               217
  1               2                 2
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    16  48
  6Q GAIN WILD-TYPE  99 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     16   48
  6Q GAIN WILD-TYPE   99  199
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              16                99
  MALE                48               199
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    59   1
  6Q GAIN WILD-TYPE 277   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     59    1
  6Q GAIN WILD-TYPE  277    6
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               59               277
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6Q GAIN MUTATED                         0                       63
  6Q GAIN WILD-TYPE                       2                      290
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6Q GAIN MUTATED                                  1
  6Q GAIN WILD-TYPE                                6
D12V9, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      63               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
  6Q GAIN MUTATED    56   2   1   5
  6Q GAIN WILD-TYPE 262  13   0  16
D12V10, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              56               262
  R1               2                13
  R2               1                 0
  RX               5                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
  6Q GAIN MUTATED                                  0    32
  6Q GAIN WILD-TYPE                                1   125
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           5    27
  6Q GAIN WILD-TYPE                        12   150
D12V11, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         32               125
  BLACK OR AFRICAN AMERICAN                      5                12
  WHITE                                         27               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"
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     5  57
  6Q GAIN WILD-TYPE   8 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5   57
  6Q GAIN WILD-TYPE    8  275
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 8
  NOT HISPANIC OR LATINO              57               275
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    67  39
  7P GAIN WILD-TYPE 162  90
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              106               252 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               39                90 
$`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        22.92        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-5264 TCGA-CC-A3MB TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HU 
        3.35        10.36         8.94        13.12        12.56        11.31 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1E9 
        8.15        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-AAVV TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66Y TCGA-ED-A7PX 
       80.71        64.77        49.48        53.69         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
       12.82        14.04         1.84         0.62         9.96        22.85 
TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
        6.38         0.33        81.73        13.68        51.06        28.27 
TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       58.49        22.13        19.53        20.42        17.10        22.06 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-LG-A6GG 
       14.70        11.80         8.75         2.14        21.60        12.72 
TCGA-MI-A75G TCGA-NI-A8LF TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       22.95        26.27        15.98        10.75         0.99        12.99 
TCGA-WX-AA46 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D1 
       24.85        22.78        13.55         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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        11.74        38.40         1.18         8.55 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
        0.66        17.10        14.76         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        23.38         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        45.93         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 
        4.24         3.19         3.39         4.24         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF 
        9.96        11.93        11.41         9.99         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV 
        9.83        12.00         8.61         9.14         4.60         9.17 
TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B 
        6.94        37.78        83.57        53.33         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       21.76        79.40        66.31        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X 
       49.15         6.02        18.35        13.64        27.19        55.69 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81         7.66        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
        0.36        30.61        32.52        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-A73C TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
       23.93         9.30        23.05        35.67        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH 
       11.41        75.65        76.41        55.40        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-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       47.67        18.54        21.63        44.22        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-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-AADU TCGA-DD-AADV TCGA-DD-AADW 
       15.06        14.33        66.67        18.21        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.25        18.15        20.98        19.99        21.17        21.83 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       25.08        26.63        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-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       62.47        66.25        65.39        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       13.91        13.35         0.20        13.15        13.41        13.35 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK 
        0.20        18.74        19.99        20.61        19.59        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-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y 
       12.03         0.03         0.39        53.79        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       21.53        25.64         5.92        19.23        25.25        22.95 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       12.23        13.55         0.89        11.87        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       11.80         2.14        31.27        29.79        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        24.56        20.71         7.53        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        36.10         0.76        17.59 
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-WX-AA44 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       20.22        18.28        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        79.30        11.21 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.20              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           114.35            120.82 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           18.755            20.055 
[1] "0.2 - 114.3 (18.8)" "0.0 - 120.8 (20.1)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED        48       27         0         19          4          4
  7P GAIN WILD-TYPE     123       58         3         41          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                 48               123
  STAGE II                27                58
  STAGE III                0                 3
  STAGE IIIA              19                41
  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      51  31  24   3
  7P GAIN WILD-TYPE   131  61  50   9
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              51               131
  T2                 31                61
  T3                 24                50
  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    70   2
  7P GAIN WILD-TYPE 180   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     70    2
  7P GAIN WILD-TYPE  180    1
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              70               180
  1               2                 1
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    80   1
  7P GAIN WILD-TYPE 181   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     80    1
  7P GAIN WILD-TYPE  181    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              80               181
  1               1                 3
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    39  70
  7P GAIN WILD-TYPE  76 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     39   70
  7P GAIN WILD-TYPE   76  177
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              39                76
  MALE                70               177
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   101   2
  7P GAIN WILD-TYPE 235   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    101    2
  7P GAIN WILD-TYPE  235    5
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              101               235
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7P GAIN MUTATED                         0                      108
  7P GAIN WILD-TYPE                       2                      245
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7P GAIN MUTATED                                  1
  7P GAIN WILD-TYPE                                6
D13V9, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     108               245
  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    96   6   0   6
  7P GAIN WILD-TYPE 222   9   1  15
D13V10, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              96               222
  R1               6                 9
  R2               0                 1
  RX               6                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1    42
  7P GAIN WILD-TYPE                                0   115
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           5    59
  7P GAIN WILD-TYPE                        12   118
D13V11, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         42               115
  BLACK OR AFRICAN AMERICAN                      5                12
  WHITE                                         59               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"
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     5 101
  7P GAIN WILD-TYPE   8 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5  101
  7P GAIN WILD-TYPE    8  231
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 8
  NOT HISPANIC OR LATINO             101               231
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    65  41
  7Q GAIN WILD-TYPE 164  88
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              106               252 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               41                88 
$`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 
       49.84        20.81        22.92        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-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A5UE 
        0.66         2.86         3.35         9.86        10.36         8.94 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A118 TCGA-DD-A11A 
       13.12        12.56        11.31         8.15       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-AAVV TCGA-DD-AAVX TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66Y 
       80.71        56.48        49.48        53.69        29.92         9.73 
TCGA-ED-A7PY TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
       12.82        19.99        20.61         0.62         9.96        22.85 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CG 
        8.12         6.38        51.06        28.27        58.49        22.13 
TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-AAV1 
       19.53        20.42        17.10        22.06        14.70        11.80 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A4U2 
        8.75         2.14        21.60        12.72        22.95        58.88 
TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       26.27        21.04         1.71        10.75         0.99        12.99 
TCGA-WX-AA46 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D1 
       24.85        22.78        13.55         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        38.40         1.18         8.55         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
       17.10        14.76         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        23.38         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        45.93         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         4.24         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC 
        3.39         4.24         3.32         9.96        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK 
        9.99         7.13        21.34         9.83        12.00         8.61 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 
        9.14         4.60         9.17         6.94        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA 
       83.57        53.33         7.33         0.46        21.76        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        13.64        27.19        55.69        25.81         7.66 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL 
       30.61        32.52        30.97        30.15        30.51        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       29.56        73.81       108.76         0.30        80.75        23.93 
TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        9.30        22.78        35.67        13.48         0.53        11.41 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       76.41        55.40        15.42         6.41        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS 
        3.52        58.16        42.81        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-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-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.67        35.05        34.49        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        18.21        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.25        18.15        20.98        19.99        21.17        21.83 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        23.64        25.78        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVY 
       89.69        82.62        59.93        72.39        76.18        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       62.47        66.25        65.39        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.20         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK 
       13.35         1.84         0.20        18.74        19.59        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        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-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       30.74        14.86        21.53        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       25.25        22.95        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
       15.78        15.65        12.23        13.55         0.89        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83        11.80         2.14        31.27        29.79 
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        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB 
        7.53        10.85        17.69        21.01         3.09        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        36.10         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       19.76        16.44        15.98         7.04        10.32        11.34 
TCGA-WX-AA44 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       20.22        18.28        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        79.30        11.21 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.39              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           114.35            120.82 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           20.205            19.315 
[1] "0.4 - 114.3 (20.2)" "0.0 - 120.8 (19.3)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED        46       29         0         20          3          4
  7Q GAIN WILD-TYPE     125       56         3         40          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                 46               125
  STAGE II                29                56
  STAGE III                0                 3
  STAGE IIIA              20                40
  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      49  33  24   3
  7Q GAIN WILD-TYPE   133  59  50   9
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              49               133
  T2                 33                59
  T3                 24                50
  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    71   2
  7Q GAIN WILD-TYPE 179   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     71    2
  7Q GAIN WILD-TYPE  179    1
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              71               179
  1               2                 1
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    76   1
  7Q GAIN WILD-TYPE 185   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     76    1
  7Q GAIN WILD-TYPE  185    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              76               185
  1               1                 3
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    35  74
  7Q GAIN WILD-TYPE  80 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     35   74
  7Q GAIN WILD-TYPE   80  173
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              35                80
  MALE                74               173
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   101   3
  7Q GAIN WILD-TYPE 235   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    101    3
  7Q GAIN WILD-TYPE  235    4
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              101               235
  YES               3                 4
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7Q GAIN MUTATED                         0                      108
  7Q GAIN WILD-TYPE                       2                      245
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7Q GAIN MUTATED                                  1
  7Q GAIN WILD-TYPE                                6
D14V9, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     108               245
  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    96   5   0   6
  7Q GAIN WILD-TYPE 222  10   1  15
D14V10, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              96               222
  R1               5                10
  R2               0                 1
  RX               6                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
  7Q GAIN MUTATED                                  1    40
  7Q GAIN WILD-TYPE                                0   117
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           6    61
  7Q GAIN WILD-TYPE                        11   116
D14V11, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         40               117
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         61               116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     6 101
  7Q GAIN WILD-TYPE   7 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6  101
  7Q GAIN WILD-TYPE    7  231
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 7
  NOT HISPANIC OR LATINO             101               231
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    52  25
  8P GAIN WILD-TYPE 177 104
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               77               281 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               25               104 
$`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        14.76        48.99 
TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A5UC 
       46.78         4.24         3.35         3.32        10.36        11.41 
TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1E9 
        8.94        21.34        12.00         7.33         2.60        90.71 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A3A1 TCGA-DD-A4NN TCGA-DD-A4NO 
       19.79        12.95         6.02         7.66        29.56        73.81 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACI TCGA-DD-AACJ 
       12.26        80.75         0.53        12.53        53.19        69.11 
TCGA-DD-AACT TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 
       51.35         5.62        18.54        21.63        44.22        22.09 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADL TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE1 
       40.47        39.52        20.91        66.67        18.21        18.15 
TCGA-DD-AAE3 TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       18.61        50.33        35.08        80.71        76.18        56.48 
TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XP TCGA-ED-A82E 
       49.48        29.92        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-GJ-A3OU 
       20.42        11.87        15.78        11.80        13.55        22.92 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75H TCGA-MR-A8JO 
       11.80        21.60        31.27        12.03        24.56        10.85 
TCGA-UB-A7MC TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-ZS-A9CD 
       16.44         0.99        12.99        20.22        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        49.84        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        38.40        20.81        22.92         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        17.10         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 
       23.38         1.12        69.57         5.03        44.42        45.93 
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-CC-A5UD 
        3.39         4.24         9.86         9.96        11.93         9.99 
TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        7.13         9.83        13.12        12.56         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        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        26.63 
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 
       26.93        28.08        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-A7M5 
       19.53        19.23        25.25        17.10        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 
       20.78        14.14         1.84        15.65        12.23         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14        11.87         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 
       37.71        20.75        17.06        16.83         2.14        29.79 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       12.72        13.97         9.57        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
        7.53        58.88        26.27        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        36.10 
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-WX-AA47 TCGA-XR-A8TF 
       10.75        10.32        11.34        24.85        18.28        22.78 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        40.80        79.30        11.21 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.39              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            90.71            120.82 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            18.61             19.99 
[1] "0.4 - 90.7 (18.6)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P GAIN MUTATED        39       18         0         15          1          1
  8P GAIN WILD-TYPE     132       67         3         45          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                 39               132
  STAGE II                18                67
  STAGE III                0                 3
  STAGE IIIA              15                45
  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      39  18  18   2
  8P GAIN WILD-TYPE   143  74  56  10
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              39               143
  T2                 18                74
  T3                 18                56
  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    62   0
  8P GAIN WILD-TYPE 188   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     62    0
  8P GAIN WILD-TYPE  188    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              62               188
  1               0                 3
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    63   1
  8P GAIN WILD-TYPE 198   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     63    1
  8P GAIN WILD-TYPE  198    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              63               198
  1               1                 3
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    17  61
  8P GAIN WILD-TYPE  98 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     17   61
  8P GAIN WILD-TYPE   98  186
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              17                98
  MALE                61               186
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    69   3
  8P GAIN WILD-TYPE 267   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     69    3
  8P GAIN WILD-TYPE  267    4
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               69               267
  YES               3                 4
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8P GAIN MUTATED                         1                       75
  8P GAIN WILD-TYPE                       1                      278
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8P GAIN MUTATED                                  2
  8P GAIN WILD-TYPE                                5
D15V9, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      75               278
  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    66   2   1   7
  8P GAIN WILD-TYPE 252  13   0  14
D15V10, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              66               252
  R1               2                13
  R2               1                 0
  RX               7                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    41
  8P GAIN WILD-TYPE                                1   116
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           1    34
  8P GAIN WILD-TYPE                        16   143
D15V11, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         41               116
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         34               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"
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     4  70
  8P GAIN WILD-TYPE   9 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4   70
  8P GAIN WILD-TYPE    9  262
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 9
  NOT HISPANIC OR LATINO              70               262
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   120  63
  8Q GAIN WILD-TYPE 109  66
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              183               175 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               63                66 
$`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        17.10        14.76 
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-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
       36.66         4.24         3.35         3.32         9.86        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.93        11.41         8.94        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS 
       13.12         8.61         9.14         4.60         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        8.15        79.73        53.33       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       21.76        90.71        19.79        11.47        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 
        6.02        13.64        21.14         5.62        19.76         7.66 
TCGA-DD-A3A3 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ 
       17.59         0.36        90.28        30.97        26.83        30.51 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73D 
       29.56        73.81        12.26         0.30        80.75        22.78 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD 
      114.35         0.53        11.41        75.65        76.41        12.53 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN 
       15.42         6.41        53.19        69.11        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 
       61.68        13.64        51.35         5.62        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-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       39.52        35.67        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 
       14.89        14.33        66.67        18.21        18.25        18.15 
TCGA-DD-AAE3 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       18.61        21.83        23.74        25.08        26.63        23.64 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       50.33        35.08        59.93        80.71        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-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       29.92        13.35         9.73         0.20        13.15        13.41 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        1.84        18.74        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.93        22.85        14.40        23.97         8.12         6.38 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z 
       81.73         0.39        51.06        30.74        58.49        21.53 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 
       22.13        19.53        25.25        22.95        20.42        20.78 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A3OU 
       11.87        15.78        11.80        13.55         8.75        22.92 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QD 
        2.99        16.83        11.80        21.60        31.27        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-O8-A75V 
        9.57        16.67        24.56        20.71        10.85        17.69 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       19.04        15.39        36.10        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       10.75         0.99        12.99        20.22        13.55        35.77 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       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        49.84        11.74        38.40        20.81        22.92 
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        23.38         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        45.93        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-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IJ 
        3.39         4.24         9.96         9.99         7.13        12.56 
TCGA-CC-A8HU TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA 
       11.31        37.78        83.57         0.46        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39W 
       66.31        75.65        49.15        33.04        18.35        27.19 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       55.69        25.81        70.06        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NK 
       13.78        30.61        33.14        32.52        30.15        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       56.25       108.76        78.84        23.93         9.30        23.05 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF 
        1.45        35.67        13.48        55.40        63.48        12.00 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
        0.30         3.52        14.20        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 
       46.82         5.59        47.67         4.50        42.58        40.08 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADP TCGA-DD-AADS TCGA-DD-AADV 
        3.78        37.64        35.05        15.06        15.58        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       19.30        18.25        20.98        19.99         4.64        21.17 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       18.90        15.72        25.78        79.07        89.69        82.62 
TCGA-DD-AAVU TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       72.39        26.93        28.08        13.91         0.20        12.82 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A26S TCGA-FV-A23B TCGA-FV-A2QR 
       14.04        13.35         0.20        19.99        60.89        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U 
       27.88        12.03         0.03         0.33        13.68        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SM 
       28.27        14.86        25.64         5.92        19.23        17.10 
TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV2 
       22.06        14.70        14.14         1.84        15.65        12.23 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 
        0.89         2.14        11.87         1.02         2.20        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       20.75        17.06         2.14        29.79        12.72        13.97 
TCGA-MI-A75G TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
       22.95         7.53        58.88        26.27        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-WX-AA47 TCGA-XR-A8TF 
        7.04        10.32        11.34        24.85        18.28        22.78 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       25.71        23.21        35.87         0.69        25.15        40.80 
TCGA-ZS-A9CF 
       79.30 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.20              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           114.35            120.82 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            18.74             20.75 
[1] "0.2 - 114.3 (18.7)" "0.0 - 120.8 (20.8)"
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED        86       50         0         33          3          2
  8Q GAIN WILD-TYPE      85       35         3         27          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                 86                85
  STAGE II                50                35
  STAGE III                0                 3
  STAGE IIIA              33                27
  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      89 53 38  4
  8Q GAIN WILD-TYPE    93 39 36  8
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              89                93
  T2                 53                39
  T3                 38                36
  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   136   1
  8Q GAIN WILD-TYPE 114   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    136    1
  8Q GAIN WILD-TYPE  114    2
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             136               114
  1               1                 2
[1] 2 2
[1] FALSE
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   138   2
  8Q GAIN WILD-TYPE 123   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    138    2
  8Q GAIN WILD-TYPE  123    2
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             138               123
  1               2                 2
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    44 141
  8Q GAIN WILD-TYPE  71 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     44  141
  8Q GAIN WILD-TYPE   71  106
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              44                71
  MALE               141               106
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   168   6
  8Q GAIN WILD-TYPE 168   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    168    6
  8Q GAIN WILD-TYPE  168    1
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              168               168
  YES               6                 1
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8Q GAIN MUTATED                         1                      182
  8Q GAIN WILD-TYPE                       1                      171
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8Q GAIN MUTATED                                  2
  8Q GAIN WILD-TYPE                                5
D16V9, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                     182               171
  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   162   8   1  11
  8Q GAIN WILD-TYPE 156   7   0  10
D16V10, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             162               156
  R1               8                 7
  R2               1                 0
  RX              11                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    91
  8Q GAIN WILD-TYPE                                0    66
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          10    78
  8Q GAIN WILD-TYPE                         7    99
D16V11, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         91                66
  BLACK OR AFRICAN AMERICAN                     10                 7
  WHITE                                         78                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     7 171
  8Q GAIN WILD-TYPE   6 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      7  171
  8Q GAIN WILD-TYPE    6  161
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 6
  NOT HISPANIC OR LATINO             171               161
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    12   6
  9P GAIN WILD-TYPE 217 123
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               18               340 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6               123 
$`9P GAIN MUTATED`
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A7II TCGA-CC-A7IK 
        0.66        17.10         0.66         3.35        13.12         8.61 
TCGA-CC-A8HV TCGA-DD-A3A7 TCGA-DD-A4NV TCGA-DD-AACB TCGA-DD-AADJ TCGA-DD-AAVV 
        9.17        13.78        78.84        76.41        35.05        80.71 
TCGA-ED-A66Y TCGA-ED-A7XO TCGA-EP-A2KB TCGA-G3-A25U TCGA-KR-A7K2 TCGA-ZP-A9D1 
        9.73        14.04        19.59        53.79        21.60         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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        38.40        20.81        22.92 
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 
       14.76         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        23.38 
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        45.93         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         4.24         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         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS 
       12.00        12.56         9.14         4.60        11.31         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        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-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-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-A73A 
       73.81       108.76        12.26         0.30        80.75        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-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-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-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       25.08        26.63        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        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20        12.82         0.20        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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       17.10        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89         8.75         2.14        11.87        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       11.80         2.14        31.27        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        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 
       36.10         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-A9G7 
       15.98         7.04        10.75        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 
       12.99        20.22        24.85        18.28        22.78        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        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.66              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            80.71            120.82 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            13.91             19.99 
[1] "0.7 - 80.7 (13.9)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.1"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P GAIN MUTATED         5        4         0          7          1          0
  9P GAIN WILD-TYPE     166       81         3         53          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               166
  STAGE II                 4                81
  STAGE III                0                 3
  STAGE IIIA               7                53
  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   5   8   0
  9P GAIN WILD-TYPE   176  87  66  12
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               6               176
  T2                  5                87
  T3                  8                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"
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    16   0
  9P GAIN WILD-TYPE 234   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     16    0
  9P GAIN WILD-TYPE  234    3
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              16               234
  1               0                 3
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    15   1
  9P GAIN WILD-TYPE 246   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15    1
  9P GAIN WILD-TYPE  246    3
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              15               246
  1               1                 3
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     8  11
  9P GAIN WILD-TYPE 107 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      8   11
  9P GAIN WILD-TYPE  107  236
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               8               107
  MALE                11               236
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    19   0
  9P GAIN WILD-TYPE 317   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     19    0
  9P GAIN WILD-TYPE  317    7
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               19               317
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9P GAIN MUTATED                         0                       17
  9P GAIN WILD-TYPE                       2                      336
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9P GAIN MUTATED                                  2
  9P GAIN WILD-TYPE                                5
D17V9, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      17               336
  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    16   0   0   3
  9P GAIN WILD-TYPE 302  15   1  18
D17V10, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              16               302
  R1               0                15
  R2               0                 1
  RX               3                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
  9P GAIN MUTATED                                  0    11
  9P GAIN WILD-TYPE                                1   146
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           1     6
  9P GAIN WILD-TYPE                        16   171
D17V11, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11               146
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                          6               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"
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  16
  9P GAIN WILD-TYPE  12 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   16
  9P GAIN WILD-TYPE   12  316
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              16               316
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    11   8
  9Q GAIN WILD-TYPE 218 121
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               19               339 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                8               121 
$`9Q GAIN MUTATED`
TCGA-2Y-A9GY TCGA-5R-AA1C TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A7IG TCGA-CC-A7II 
       24.89        17.10         0.66         3.35         9.83        13.12 
TCGA-CC-A7IK TCGA-CC-A8HV TCGA-DD-A3A6 TCGA-DD-A4NV TCGA-DD-AACY TCGA-DD-AADJ 
        8.61         9.17       107.11        78.84        47.67        35.05 
TCGA-DD-AAVV TCGA-ED-A66Y TCGA-EP-A2KB TCGA-G3-A25U TCGA-KR-A7K2 TCGA-WQ-A9G7 
       80.71         9.73        19.59        53.79        21.60         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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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 
       14.76         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        23.38 
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        45.93         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         4.24         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         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH 
       11.41         9.99         8.94         7.13        21.34        12.00 
TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW 
       12.56         9.14         4.60        11.31         6.94         8.15 
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 
       26.63        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 
       29.92        26.93        28.08        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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       17.10        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89         8.75         2.14        11.87        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       11.80         2.14        31.27        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        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 
       36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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        35.87        25.15        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 
            17.10             19.79 
[1] "0.7 - 107.1 (17.1)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q GAIN MUTATED         5        6         0          7          0          0
  9Q GAIN WILD-TYPE     166       79         3         53          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               166
  STAGE II                 6                79
  STAGE III                0                 3
  STAGE IIIA               7                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
  9Q GAIN MUTATED       6   7   8   0
  9Q GAIN WILD-TYPE   176  85  66  12
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               6               176
  T2                  7                85
  T3                  8                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"
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    16   0
  9Q GAIN WILD-TYPE 234   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     16    0
  9Q GAIN WILD-TYPE  234    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              16               234
  1               0                 3
[1] 2 2
[1] FALSE
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    16   1
  9Q GAIN WILD-TYPE 245   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     16    1
  9Q GAIN WILD-TYPE  245    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              16               245
  1               1                 3
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    11  10
  9Q GAIN WILD-TYPE 104 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     11   10
  9Q GAIN WILD-TYPE  104  237
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              11               104
  MALE                10               237
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    20   0
  9Q GAIN WILD-TYPE 316   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     20    0
  9Q GAIN WILD-TYPE  316    7
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               20               316
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9Q GAIN MUTATED                         0                       20
  9Q GAIN WILD-TYPE                       2                      333
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9Q GAIN MUTATED                                  1
  9Q GAIN WILD-TYPE                                6
D18V9, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      20               333
  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    18   0   0   3
  9Q GAIN WILD-TYPE 300  15   1  18
D18V10, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              18               300
  R1               0                15
  R2               0                 1
  RX               3                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
  9Q GAIN MUTATED                                  0    11
  9Q GAIN WILD-TYPE                                1   146
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           1     9
  9Q GAIN WILD-TYPE                        16   168
D18V11, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11               146
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                          9               168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  19
  9Q GAIN WILD-TYPE  12 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   19
  9Q GAIN WILD-TYPE   12  313
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              19               313
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    36  23
  10P GAIN WILD-TYPE 193 106
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                59                299 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                23                106 
$`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-5264 TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7IH 
        3.35        10.36        11.41         9.99         9.83        12.00 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A 
       11.31         9.17         8.15        79.73        37.78         2.60 
TCGA-DD-A1EL TCGA-DD-A3A9 TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AACB 
       13.64        30.61        78.84        22.78       114.35        76.41 
TCGA-DD-AACM TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN 
       58.16         5.62        44.22        40.47         3.78        29.52 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE3 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAED 
       18.87        19.30        18.61        21.83        23.74        25.08 
TCGA-DD-AAEK TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E TCGA-ED-A8O6 
       35.08        29.92        13.35         9.73        13.41         1.84 
TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.59        22.85         0.39        22.95        20.42        17.10 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-RC-A7SH TCGA-RC-A7SK 
        8.75         2.14        10.85        26.27        15.39        15.52 
TCGA-UB-A7MA TCGA-UB-A7ME TCGA-UB-AA0U TCGA-XR-A8TF TCGA-YA-A8S7 
       17.59        15.98        10.75        22.78        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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB 
       18.25        11.74        38.40        20.81        22.92         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        17.10        14.76         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        23.38         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 
       45.93         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         4.24 
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         9.86 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7II 
        9.96        11.93         8.94         7.13        21.34        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A9FS TCGA-DD-A115 
       12.56         8.61         9.14         4.60         6.94        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-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        33.14        32.52        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-A73A 
       73.81       108.76        12.26         0.30        80.75        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
        9.30        23.05         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-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-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        21.63        42.58        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.83        13.97        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-AADQ 
       34.49        20.91         0.39        14.89        15.06        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-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEB 
       20.98        19.99         4.64        21.17        18.90        15.72 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        23.64        25.78        50.33        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        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-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       26.93        28.08        13.91         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       14.04        13.15        13.35         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61         0.62         9.96        11.93        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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A6UC 
       25.64         5.92        19.53        19.23        25.25        22.06 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       14.70        20.78        11.87        14.14         1.84        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
       15.65        11.80        12.23        13.55         0.89        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83        11.80         2.14        21.60        31.27 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       29.79        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 
       22.95        24.56        20.71         7.53        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 
       21.01         3.09        21.04        19.33        19.04        36.10 
TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V 
        0.76        19.76        16.44         1.71         7.04        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        35.87         0.69        25.15 
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 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.39               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            114.35             120.82 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             15.98              20.61 
[1] "0.4 - 114.3 (16.0)" "0.0 - 120.8 (20.6)"
[1] "hr=" "1.4"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10P GAIN MUTATED        23       17         0         15          1
  10P GAIN WILD-TYPE     148       68         3         45          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                  23                148
  STAGE II                 17                 68
  STAGE III                 0                  3
  STAGE IIIA               15                 45
  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      23  20  17   1
  10P GAIN WILD-TYPE   159  72  57  11
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1               23                159
  T2                  20                 72
  T3                  17                 57
  T4                   1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    43   0
  10P GAIN WILD-TYPE 207   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     43    0
  10P GAIN WILD-TYPE  207    3
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               43                207
  1                0                  3
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    44   2
  10P GAIN WILD-TYPE 217   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     44    2
  10P GAIN WILD-TYPE  217    2
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               44                217
  1                2                  2
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    19  42
  10P GAIN WILD-TYPE  96 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     19   42
  10P GAIN WILD-TYPE   96  205
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               19                 96
  MALE                 42                205
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    54   2
  10P GAIN WILD-TYPE 282   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     54    2
  10P GAIN WILD-TYPE  282    5
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                54                282
  YES                2                  5
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10P GAIN MUTATED                         1                       59
  10P GAIN WILD-TYPE                       1                      294
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10P GAIN MUTATED                                  1
  10P GAIN WILD-TYPE                                6
D19V9, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       59                294
  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    54   3   0   4
  10P GAIN WILD-TYPE 264  12   1  17
D19V10, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               54                264
  R1                3                 12
  R2                0                  1
  RX                4                 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
  10P GAIN MUTATED                                  0    32
  10P GAIN WILD-TYPE                                1   125
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           4    25
  10P GAIN WILD-TYPE                        13   152
D19V11, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          32                125
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          25                152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     4  56
  10P GAIN WILD-TYPE   9 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4   56
  10P GAIN WILD-TYPE    9  276
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  9
  NOT HISPANIC OR LATINO               56                276
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    24  11
  10Q GAIN WILD-TYPE 205 118
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                35                323 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                118 
$`10Q GAIN MUTATED`
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A8HU TCGA-CC-A8HV 
       13.02        10.78         9.83        12.00        11.31         9.17 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A39Z TCGA-DD-A3A9 TCGA-DD-A4NV TCGA-DD-A73G 
        8.15        79.73        19.76        30.61        78.84       114.35 
TCGA-DD-AACB TCGA-DD-AADD TCGA-DD-AADN TCGA-DD-AADV TCGA-DD-AAE9 TCGA-DD-AAED 
       76.41        40.47        29.52        18.87        23.74        25.08 
TCGA-DD-AAEK TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS 
       35.08        13.35         9.73        13.41        19.59        22.85 
TCGA-FV-A4ZQ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-NI-A8LF 
        0.39        20.42        17.10         8.75         2.14        26.27 
TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-AA0U TCGA-XR-A8TF TCGA-YA-A8S7 
       15.39        17.59        10.75        22.78        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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        38.40        20.81        22.92 
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        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       14.76         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        23.38 
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        45.93         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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.39         4.24         3.35         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
       21.34        13.12        12.56         8.61         9.14         4.60 
TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        6.94        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 
       26.63        23.64        25.78        50.33        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        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 
       29.92        26.93        28.08        13.91         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-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-A5SJ TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       25.25        22.95        22.06        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       14.14         1.84        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       13.55         0.89        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
        7.53        10.85        58.88        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       21.04        19.33        19.04        15.52        36.10         0.76 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V 
       19.76        16.44         1.71        15.98         7.04        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        35.87         0.69        25.15 
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 
             17.59              19.99 
[1] "0.4 - 114.3 (17.6)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q GAIN MUTATED        12       12         0         10          1
  10Q GAIN WILD-TYPE     159       73         3         50          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                  12                159
  STAGE II                 12                 73
  STAGE III                 0                  3
  STAGE IIIA               10                 50
  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      12  13  11   1
  10Q GAIN WILD-TYPE   170  79  63  11
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1               12                170
  T2                  13                 79
  T3                  11                 63
  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 224   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     26    0
  10Q GAIN WILD-TYPE  224    3
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               26                224
  1                0                  3
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    27   2
  10Q GAIN WILD-TYPE 234   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     27    2
  10Q GAIN WILD-TYPE  234    2
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               27                234
  1                2                  2
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    14  23
  10Q GAIN WILD-TYPE 101 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     14   23
  10Q GAIN WILD-TYPE  101  224
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               14                101
  MALE                 23                224
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    31   1
  10Q GAIN WILD-TYPE 305   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     31    1
  10Q GAIN WILD-TYPE  305    6
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                31                305
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10Q GAIN MUTATED                         0                       36
  10Q GAIN WILD-TYPE                       2                      317
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10Q GAIN MUTATED                                  1
  10Q GAIN WILD-TYPE                                6
D20V9, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       36                317
  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    33   2   0   2
  10Q GAIN WILD-TYPE 285  13   1  19
D20V10, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               33                285
  R1                2                 13
  R2                0                  1
  RX                2                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   140
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           1    18
  10Q GAIN WILD-TYPE                        16   159
D20V11, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          17                140
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                          18                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"
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3  33
  10Q GAIN WILD-TYPE  10 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3   33
  10Q GAIN WILD-TYPE   10  299
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               33                299
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    11   5
  11P GAIN WILD-TYPE 218 124
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                16                342 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                124 
$`11P GAIN MUTATED`
TCGA-2Y-A9GZ TCGA-BC-A69H TCGA-BD-A3EP TCGA-CC-A7IE TCGA-CC-A7II TCGA-DD-A119 
       27.88        14.60        13.45         7.13        13.12         7.33 
TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-AAD1 TCGA-ED-A66Y TCGA-ED-A82E TCGA-FV-A4ZQ 
        5.62        78.84        18.54         9.73        13.41         0.39 
TCGA-G3-A3CG TCGA-LG-A6GG TCGA-UB-A7ME TCGA-WQ-A9G7 
       22.13        12.72        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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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 
       17.10        14.76         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 
       23.38         1.12        69.57         5.03        44.42        45.93 
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         4.24         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        4.24         3.35         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.93        11.41         9.99         8.94        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       12.00        12.56         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        9.17         6.94         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        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-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-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-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-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-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-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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       28.08        13.91        13.35         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-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-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-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-A7M5 
       25.25        22.95        20.42        17.10        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        22.92         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83        11.80         2.14        21.60 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       31.27        29.79        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 
       22.95        24.56        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       26.27        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        36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
       11.34        12.99        20.22        24.85        18.28        22.78 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        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 
            13.265             20.170 
[1] "0.4 - 78.8 (13.3)"  "0.0 - 120.8 (20.2)"
[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     164       82         3         55          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                164
  STAGE II                  3                 82
  STAGE III                 0                  3
  STAGE IIIA                5                 55
  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   175  89  67  12
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                7                175
  T2                   3                 89
  T3                   7                 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"
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     9   0
  11P GAIN WILD-TYPE 241   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      9    0
  11P GAIN WILD-TYPE  241    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                9                241
  1                0                  3
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    13   1
  11P GAIN WILD-TYPE 248   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     13    1
  11P GAIN WILD-TYPE  248    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               13                248
  1                1                  3
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     7  10
  11P GAIN WILD-TYPE 108 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7   10
  11P GAIN WILD-TYPE  108  237
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                7                108
  MALE                 10                237
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    14   0
  11P GAIN WILD-TYPE 322   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     14    0
  11P GAIN WILD-TYPE  322    7
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                14                322
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11P GAIN MUTATED                         0                       17
  11P GAIN WILD-TYPE                       2                      336
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11P GAIN MUTATED                                  0
  11P GAIN WILD-TYPE                                7
D21V9, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       17                336
  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 305  13   0  20
D21V10, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               13                305
  R1                2                 13
  R2                1                  0
  RX                1                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   149
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           1     8
  11P GAIN WILD-TYPE                        16   169
D21V11, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                149
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           8                169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  17
  11P GAIN WILD-TYPE  13 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   17
  11P GAIN WILD-TYPE   13  315
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               17                315
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    11   6
  11Q GAIN WILD-TYPE 218 123
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                341 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                123 
$`11Q GAIN MUTATED`
TCGA-2Y-A9GZ TCGA-BC-A69I TCGA-BD-A3EP TCGA-CC-A7IE TCGA-CC-A7II TCGA-DD-A119 
       27.88        12.72        13.45         7.13        13.12         7.33 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NV TCGA-DD-AAD1 TCGA-DD-AADW TCGA-DD-AAE0 
        5.62        25.81        78.84        18.54        19.30        18.25 
TCGA-ED-A66Y TCGA-ED-A82E TCGA-G3-A3CG TCGA-LG-A6GG TCGA-WQ-A9G7 
        9.73        13.41        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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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 
       17.10        14.76         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 
       23.38         1.12        69.57         5.03        44.42        45.93 
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         4.24         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        4.24         3.35         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.93        11.41         9.99         8.94        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       12.00        12.56         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        9.17         6.94         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        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-A39Z TCGA-DD-A3A1 
       13.64        21.14        27.19        55.69        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-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-A73A 
       73.81       108.76        12.26         0.30        80.75        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-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-AAD2 
       46.82         5.59        47.67         5.62         4.50        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-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-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 
       26.63        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        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        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
        0.20        12.82         0.20        14.04        13.15        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-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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       20.42        17.10        22.06        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       14.14         1.84        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89         8.75         2.14        11.87        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83        11.80         2.14        21.60        31.27        29.79 
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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        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-A7MB TCGA-UB-A7MC 
       15.52        36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 
       12.99        20.22        24.85        18.28        22.78        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        35.87         0.69        25.15 
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 

  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 
             13.41              20.12 
[1] "1.0 - 78.8 (13.4)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.4"
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     163       83         3         54          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                163
  STAGE II                  2                 83
  STAGE III                 0                  3
  STAGE IIIA                6                 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
  11Q GAIN MUTATED       8   2   8   0
  11Q GAIN WILD-TYPE   174  90  66  12
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                8                174
  T2                   2                 90
  T3                   8                 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"
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    12   0
  11Q GAIN WILD-TYPE 238   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     12    0
  11Q GAIN WILD-TYPE  238    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               12                238
  1                0                  3
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    15   1
  11Q GAIN WILD-TYPE 246   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     15    1
  11Q GAIN WILD-TYPE  246    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               15                246
  1                1                  3
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     8  10
  11Q GAIN WILD-TYPE 107 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      8   10
  11Q GAIN WILD-TYPE  107  237
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                8                107
  MALE                 10                237
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    16   0
  11Q GAIN WILD-TYPE 320   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     16    0
  11Q GAIN WILD-TYPE  320    7
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                16                320
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11Q GAIN MUTATED                         0                       18
  11Q GAIN WILD-TYPE                       2                      335
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11Q GAIN MUTATED                                  0
  11Q GAIN WILD-TYPE                                7
D22V9, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       18                335
  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 304  13   0  20
D22V10, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               14                304
  R1                2                 13
  R2                1                  0
  RX                1                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   148
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           1     8
  11Q GAIN WILD-TYPE                        16   169
D22V11, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                148
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           8                169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  17
  11Q GAIN WILD-TYPE  13 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   17
  11Q GAIN WILD-TYPE   13  315
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               17                315
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    24  16
  12P GAIN WILD-TYPE 205 113
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                40                318 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                16                113 
$`12P GAIN MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9H2 TCGA-5C-A9VG TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A5UC 
       41.79        56.91        10.78         0.66         3.35        11.41 
TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A11A 
        7.13        13.12        12.56        11.31         8.15         2.60 
TCGA-DD-A1EF TCGA-DD-A3A7 TCGA-DD-A4NR TCGA-DD-A73G TCGA-DD-AACI TCGA-DD-AACK 
       12.95        13.78         0.30       114.35        53.19         0.30 
TCGA-DD-AACZ TCGA-DD-AADF TCGA-DD-AADR TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ 
        5.62         3.78        66.67         9.73         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A3JL TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A7M9 TCGA-G3-AAV1 
       13.41         9.96        27.88        51.06         1.84        11.80 
TCGA-G3-AAV6 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75C TCGA-NI-A8LF TCGA-PD-A5DF 
        2.14        11.80        21.60         9.57        26.27        21.01 
TCGA-UB-A7MA TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-XR-A8TF 
       17.59        15.98         0.99        22.78 

$`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        49.84        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        38.40        20.81        22.92         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        17.10        14.76 
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        23.38         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        45.93         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         4.24         2.86         3.19         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD 
        3.32         9.86         9.96        10.36        11.93         9.99 
TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL 
        8.94        21.34         9.83        12.00         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        4.60         9.17         6.94        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-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-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-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       73.81       108.76        12.26        80.75        78.84        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-AACJ TCGA-DD-AACL 
       63.48        12.00        15.42         6.41        69.11         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-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-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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       28.08        13.91        13.35        12.82        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-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       19.59         0.62        11.93        22.85        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-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-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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       17.10        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.78        15.65        12.23        13.55         0.89         8.75 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        22.92         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       20.75        17.06        16.83         2.14        31.27        29.79 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       12.72        13.97        12.03        16.67        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 
       20.71         7.53        10.85        58.88        17.69         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        36.10 
TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U 
        0.76        19.76        16.44         1.71         7.04        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.32        11.34        12.99        20.22        24.85        18.28 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        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 
            11.605             20.730 
[1] "0.2 - 114.3 (11.6)" "0.0 - 120.8 (20.7)"
[1] "hr=" "1.7"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P GAIN MUTATED        16        8         0         11          3
  12P GAIN WILD-TYPE     155       77         3         49          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                  16                155
  STAGE II                  8                 77
  STAGE III                 0                  3
  STAGE IIIA               11                 49
  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      16   8  14   2
  12P GAIN WILD-TYPE   166  84  60  10
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               16                166
  T2                   8                 84
  T3                  14                 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"
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    29   0
  12P GAIN WILD-TYPE 221   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     29    0
  12P GAIN WILD-TYPE  221    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               29                221
  1                0                  3
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    31   0
  12P GAIN WILD-TYPE 230   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     31    0
  12P GAIN WILD-TYPE  230    4
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               31                230
  1                0                  4
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    16  24
  12P GAIN WILD-TYPE  99 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     16   24
  12P GAIN WILD-TYPE   99  223
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               16                 99
  MALE                 24                223
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    38   0
  12P GAIN WILD-TYPE 298   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     38    0
  12P GAIN WILD-TYPE  298    7
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                38                298
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12P GAIN MUTATED                         0                       36
  12P GAIN WILD-TYPE                       2                      317
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12P GAIN MUTATED                                  4
  12P GAIN WILD-TYPE                                3
D23V9, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       36                317
  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    34   1   0   3
  12P GAIN WILD-TYPE 284  14   1  18
D23V10, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               34                284
  R1                1                 14
  R2                0                  1
  RX                3                 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
  12P GAIN MUTATED                                  0    18
  12P GAIN WILD-TYPE                                1   139
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           2    19
  12P GAIN WILD-TYPE                        15   158
D23V11, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          18                139
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          19                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"
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1  37
  12P GAIN WILD-TYPE  12 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   37
  12P GAIN WILD-TYPE   12  295
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               37                295
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    30  16
  12Q GAIN WILD-TYPE 199 113
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                46                312 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                113 
$`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-CC-5264 TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HU 
        3.35        11.41         7.13        13.12        12.56        11.31 
TCGA-CC-A9FW TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A3A7 TCGA-DD-A4ND 
        8.15         2.60        12.95        33.04        13.78        90.28 
TCGA-DD-A4NH TCGA-DD-A4NR TCGA-DD-A73G TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACY 
       30.15         0.30       114.35        53.19         0.30        47.67 
TCGA-DD-AACZ TCGA-DD-AADR TCGA-DD-AAEI TCGA-DD-AAVV TCGA-ED-A66Y TCGA-ED-A7PX 
        5.62        66.67        50.33        80.71         9.73         0.20 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A3JL TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A7M9 
        0.20        13.41         9.96        27.88        51.06         1.84 
TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75C TCGA-NI-A8LF 
       11.80         2.14        11.80        21.60         9.57        26.27 
TCGA-PD-A5DF TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-XR-A8TF 
       21.01        15.98         0.99        22.78 

$`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        49.84        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       38.40        20.81        22.92         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        17.10        14.76         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        23.38         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        45.93        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         4.24 
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         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF 
        9.96        10.36        11.93         9.99         8.94        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV 
        9.83        12.00         8.61         9.14         4.60         9.17 
TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        6.94        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        11.47        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
        6.02        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-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        30.97        26.83        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        73.81       108.76        12.26        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-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-AACJ 
       12.53        63.48        12.00        15.42         6.41        69.11 
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-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-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-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        26.63        23.64 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        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        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
       13.91        13.35        12.82        14.04        13.15        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-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-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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       22.06        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
       15.65        12.23        13.55         0.89         8.75        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06        16.83         2.14        31.27        29.79        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       13.97        12.03        16.67        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 
        7.53        10.85        58.88        17.69         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        36.10         0.76 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U 
       17.59        19.76        16.44         1.71         7.04        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.32        11.34        12.99        20.22        24.85        18.28 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        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 
            12.755             20.170 
[1] "0.2 - 120.8 (12.8)" "0.0 - 113.0 (20.2)"
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q GAIN MUTATED        19        8         0         12          4
  12Q GAIN WILD-TYPE     152       77         3         48          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                  19                152
  STAGE II                  8                 77
  STAGE III                 0                  3
  STAGE IIIA               12                 48
  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      20   8  16   2
  12Q GAIN WILD-TYPE   162  84  58  10
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1               20                162
  T2                   8                 84
  T3                  16                 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"
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    33   1
  12Q GAIN WILD-TYPE 217   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     33    1
  12Q GAIN WILD-TYPE  217    2
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               33                217
  1                1                  2
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    37   0
  12Q GAIN WILD-TYPE 224   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     37    0
  12Q GAIN WILD-TYPE  224    4
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               37                224
  1                0                  4
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    18  28
  12Q GAIN WILD-TYPE  97 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     18   28
  12Q GAIN WILD-TYPE   97  219
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               18                 97
  MALE                 28                219
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    43   0
  12Q GAIN WILD-TYPE 293   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     43    0
  12Q GAIN WILD-TYPE  293    7
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                43                293
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12Q GAIN MUTATED                         0                       43
  12Q GAIN WILD-TYPE                       2                      310
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12Q GAIN MUTATED                                  3
  12Q GAIN WILD-TYPE                                4
D24V9, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       43                310
  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    41   0   0   3
  12Q GAIN WILD-TYPE 277  15   1  18
D24V10, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               41                277
  R1                0                 15
  R2                0                  1
  RX                3                 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
  12Q GAIN MUTATED                                  0    20
  12Q GAIN WILD-TYPE                                1   137
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           2    23
  12Q GAIN WILD-TYPE                        15   154
D24V11, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          20                137
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          23                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"
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  41
  12Q GAIN WILD-TYPE  11 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   41
  12Q GAIN WILD-TYPE   11  291
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               41                291
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    11  11
  13Q GAIN WILD-TYPE 218 118
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                336 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                11                118 
$`13Q GAIN MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-BC-A3KF TCGA-BD-A3EP TCGA-CC-5263 TCGA-CC-A7IE 
       41.79        27.88         0.26        13.45         4.24         7.13 
TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A3A7 TCGA-DD-AACB TCGA-DD-AACO TCGA-DD-AAE3 
       45.11        33.04        13.78        76.41        61.68        18.61 
TCGA-DD-AAVW TCGA-ED-A66Y TCGA-EP-A3JL TCGA-FV-A23B TCGA-G3-AAV1 TCGA-G3-AAV6 
       76.18         9.73         9.96        60.89        11.80         2.14 
TCGA-RC-A7S9 TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WX-AA44 
       21.04        36.10        16.44        20.22 

$`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        49.84        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        38.40        20.81        22.92         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        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       14.76         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        23.38 
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        45.93        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-5264 
        0.66         4.24         2.86         3.19         3.39         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        9.99         8.94        21.34         9.83        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.56         8.61         9.14         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        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-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        49.15         6.02        18.35        13.64        21.14 
TCGA-DD-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-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-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-AACP TCGA-DD-AACQ 
        0.30         3.52        58.16        42.81        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-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-AAEK TCGA-DD-AAVP 
       26.63        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        80.71        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 
       29.92        26.93        28.08        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-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-A2QQ TCGA-FV-A2QR 
        0.62        11.93        22.85        14.40        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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       17.10        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        15.78        15.65        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       21.60        31.27        29.79        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        22.95        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52         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-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
       11.34         0.99        12.99        24.85        18.28        22.78 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        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 
            19.415             19.760 
[1] "0.3 - 76.4 (19.4)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.5"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q GAIN MUTATED        11        3         0          5          1
  13Q GAIN WILD-TYPE     160       82         3         55          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                  11                160
  STAGE II                  3                 82
  STAGE III                 0                  3
  STAGE IIIA                5                 55
  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      12   4   6   1
  13Q GAIN WILD-TYPE   170  88  68  11
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               12                170
  T2                   4                 88
  T3                   6                 68
  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 232   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     18    1
  13Q GAIN WILD-TYPE  232    2
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               18                232
  1                1                  2
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    17   1
  13Q GAIN WILD-TYPE 244   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     17    1
  13Q GAIN WILD-TYPE  244    3
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               17                244
  1                1                  3
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    11  12
  13Q GAIN WILD-TYPE 104 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     11   12
  13Q GAIN WILD-TYPE  104  235
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               11                104
  MALE                 12                235
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    21   1
  13Q GAIN WILD-TYPE 315   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     21    1
  13Q GAIN WILD-TYPE  315    6
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                21                315
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  13Q GAIN MUTATED                         0                       23
  13Q GAIN WILD-TYPE                       2                      330
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  13Q GAIN MUTATED                                  0
  13Q GAIN WILD-TYPE                                7
D25V9, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       23                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
  13Q GAIN MUTATED    19   0   0   3
  13Q GAIN WILD-TYPE 299  15   1  18
D25V10, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               19                299
  R1                0                 15
  R2                0                  1
  RX                3                 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
  13Q GAIN MUTATED                                  0     9
  13Q GAIN WILD-TYPE                                1   148
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           2    11
  13Q GAIN WILD-TYPE                        15   166
D25V11, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                148
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          11                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"
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     2  19
  13Q GAIN WILD-TYPE  11 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2   19
  13Q GAIN WILD-TYPE   11  313
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               19                313
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    13  10
  14Q GAIN WILD-TYPE 216 119
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                23                335 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                10                119 
$`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         9.86        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        21.60        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        49.84        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG 
       38.40        22.92         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        17.10        14.76         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        23.38         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        45.93         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         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA 
        3.19         3.39         4.24         3.35         3.32         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.14         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       79.73        83.57        53.33       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        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-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        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-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-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.25        18.15        20.98        19.99        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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY 
       26.93        28.08        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-A7M5 
       25.25        22.95        20.42        17.10        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
       11.80        12.23        13.55         0.89         8.75        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83        11.80         2.14        31.27        29.79 
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        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       24.56        20.71         7.53        10.85        58.88        26.27 
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        36.10         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-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
        0.99        12.99        20.22        24.85        18.28        22.78 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        35.87         0.69        25.15 
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 
              2.14               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             90.28             120.82 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             20.81              19.76 
[1] "2.1 - 90.3 (20.8)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
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     160       81         3         55          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                160
  STAGE II                  4                 81
  STAGE III                 0                  3
  STAGE IIIA                5                 55
  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   170  88  67  12
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1               12                170
  T2                   4                 88
  T3                   7                 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"
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    15   0
  14Q GAIN WILD-TYPE 235   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15    0
  14Q GAIN WILD-TYPE  235    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               15                235
  1                0                  3
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    13   1
  14Q GAIN WILD-TYPE 248   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     13    1
  14Q GAIN WILD-TYPE  248    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               13                248
  1                1                  3
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    10  13
  14Q GAIN WILD-TYPE 105 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10   13
  14Q GAIN WILD-TYPE  105  234
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               10                105
  MALE                 13                234
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    21   0
  14Q GAIN WILD-TYPE 315   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     21    0
  14Q GAIN WILD-TYPE  315    7
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                21                315
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  14Q GAIN MUTATED                         0                       21
  14Q GAIN WILD-TYPE                       2                      332
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  14Q GAIN MUTATED                                  2
  14Q GAIN WILD-TYPE                                5
D26V9, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       21                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
  14Q GAIN MUTATED    20   1   1   1
  14Q GAIN WILD-TYPE 298  14   0  20
D26V10, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               20                298
  R1                1                 14
  R2                1                  0
  RX                1                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   149
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           3    12
  14Q GAIN WILD-TYPE                        14   165
D26V11, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                149
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          12                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"
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  20
  14Q GAIN WILD-TYPE  12 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   20
  14Q GAIN WILD-TYPE   12  312
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               20                312
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    23  10
  15Q GAIN WILD-TYPE 206 119
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                325 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                119 
$`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-CC-A5UE TCGA-CC-A7IF TCGA-DD-A4NI 
       23.38        22.36         9.86         8.94        21.34        26.83 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AADU 
       78.84       114.35        76.41        13.64         5.62        18.21 
TCGA-DD-AAE3 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEK TCGA-ED-A66X TCGA-ED-A8O6 
       18.61        21.83        18.90        35.08        13.35         1.84 
TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A6UC TCGA-MI-A75G 
       22.85         0.39        51.06        58.49        22.06        22.95 
TCGA-MR-A8JO TCGA-RC-A7SK TCGA-WQ-AB4B 
       10.85        15.52        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        49.84        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-4R-AA8I 
       38.40        20.81        22.92         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        17.10        14.76         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        45.93 
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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.35         3.32         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IH 
       11.93        11.41         9.99         7.13         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       13.12        12.56         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        9.17         6.94         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       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-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-A4NJ TCGA-DD-A4NK 
       32.52        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-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-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-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
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-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-AADV TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       23.74        15.72        25.08        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        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        29.92        26.93        28.08 
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-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-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-A25U 
       12.03         0.03         0.33        81.73        13.68        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       17.10        14.70        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        8.75         2.14        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        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        24.56        20.71         7.53 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.33        19.04        15.39        36.10         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-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.32        11.34         0.99        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        25.15        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.39               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            114.35             120.82 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             21.83              19.59 
[1] "0.4 - 114.3 (21.8)" "0.0 - 120.8 (19.6)"
[1] "hr=" "1.2"
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     158       76         3         54          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                158
  STAGE II                  9                 76
  STAGE III                 0                  3
  STAGE IIIA                6                 54
  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   169  81  67  10
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1               13                169
  T2                  11                 81
  T3                   7                 67
  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 226   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     24    0
  15Q GAIN WILD-TYPE  226    3
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               24                226
  1                0                  3
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    25   0
  15Q GAIN WILD-TYPE 236   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     25    0
  15Q GAIN WILD-TYPE  236    4
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               25                236
  1                0                  4
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     9  24
  15Q GAIN WILD-TYPE 106 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9   24
  15Q GAIN WILD-TYPE  106  223
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                9                106
  MALE                 24                223
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    31   0
  15Q GAIN WILD-TYPE 305   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     31    0
  15Q GAIN WILD-TYPE  305    7
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                31                305
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  15Q GAIN MUTATED                         1                       32
  15Q GAIN WILD-TYPE                       1                      321
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  15Q GAIN MUTATED                                  0
  15Q GAIN WILD-TYPE                                7
D27V9, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       32                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
  15Q GAIN MUTATED    31   1   0   1
  15Q GAIN WILD-TYPE 287  14   1  20
D27V10, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               31                287
  R1                1                 14
  R2                0                  1
  RX                1                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   142
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           0    17
  15Q GAIN WILD-TYPE                        17   160
D27V11, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          15                142
  BLACK OR AFRICAN AMERICAN                       0                 17
  WHITE                                          17                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"
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2  30
  15Q GAIN WILD-TYPE  11 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2   30
  15Q GAIN WILD-TYPE   11  302
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               30                302
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    21   8
  16P GAIN WILD-TYPE 208 121
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                29                329 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 8                121 
$`16P GAIN MUTATED`
TCGA-2Y-A9GY TCGA-3K-AAZ8 TCGA-5R-AA1D TCGA-BC-A10R TCGA-BC-A112 TCGA-CC-A7IK 
       24.89        13.02        14.76        10.13         5.03         8.61 
TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1EL TCGA-DD-A3A5 TCGA-DD-AACI TCGA-DD-AACT 
       79.73         2.60        13.64       102.74        53.19        51.35 
TCGA-DD-AADN TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAVV TCGA-DD-AAW0 TCGA-ED-A459 
       29.52        18.61        19.99        80.71        66.25        29.92 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SM TCGA-G3-AAV1 
        0.20        13.41        13.68        51.06        17.10        11.80 
TCGA-KR-A7K2 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-UB-A7MB TCGA-UB-AA0U 
       21.60        10.85        26.27        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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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        17.10 
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        23.38         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        45.93         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-5264 
        4.24         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       13.12        12.56         9.14         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        6.94         8.15        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       49.15         6.02        33.04        18.35        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-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       17.59        20.12       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        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-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-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-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-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-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91         0.39        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-AAE0 
       15.58        18.21        18.87        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.15        20.98         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        26.63        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-AAW1 
       72.39        76.18        56.48        64.77        62.47        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        53.69        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
        9.73         0.20        12.82        14.04        13.15        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-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-A25U TCGA-G3-A25V 
        0.03         0.33        81.73         0.39        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        25.25        22.95        20.42 
TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       22.06        14.70        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.78        15.65        12.23        13.55         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       31.27        29.79        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        22.95        24.56        20.71         7.53        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-A7MC 
       15.39        15.52        36.10         0.76        17.59        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
        1.71        15.98         7.04        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 
       12.99        20.22        24.85        18.28        22.78        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        35.87         0.69        25.15 
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 

  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 
             18.61              19.79 
[1] "0.2 - 102.7 (18.6)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED        10       10         1          4          1
  16P GAIN WILD-TYPE     161       75         2         56          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                161
  STAGE II                 10                 75
  STAGE III                 1                  2
  STAGE IIIA                4                 56
  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  10   8   1
  16P GAIN WILD-TYPE   172  82  66  11
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1               10                172
  T2                  10                 82
  T3                   8                 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"
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    19   0
  16P GAIN WILD-TYPE 231   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     19    0
  16P GAIN WILD-TYPE  231    3
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               19                231
  1                0                  3
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    20   0
  16P GAIN WILD-TYPE 241   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     20    0
  16P GAIN WILD-TYPE  241    4
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               20                241
  1                0                  4
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     9  20
  16P GAIN WILD-TYPE 106 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9   20
  16P GAIN WILD-TYPE  106  227
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                9                106
  MALE                 20                227
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    26   2
  16P GAIN WILD-TYPE 310   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     26    2
  16P GAIN WILD-TYPE  310    5
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                26                310
  YES                2                  5
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16P GAIN MUTATED                         1                       27
  16P GAIN WILD-TYPE                       1                      326
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16P GAIN MUTATED                                  1
  16P GAIN WILD-TYPE                                6
D28V9, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       27                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
  16P GAIN MUTATED    25   2   0   2
  16P GAIN WILD-TYPE 293  13   1  19
D28V10, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               25                293
  R1                2                 13
  R2                0                  1
  RX                2                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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    12
  16P GAIN WILD-TYPE                                1   145
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           3    14
  16P GAIN WILD-TYPE                        14   163
D28V11, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                145
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          14                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"
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  27
  16P GAIN WILD-TYPE  13 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   27
  16P GAIN WILD-TYPE   13  305
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               27                305
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    11   4
  16Q GAIN WILD-TYPE 218 125
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                15                343 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                125 
$`16Q GAIN MUTATED`
TCGA-3K-AAZ8 TCGA-5R-AA1D TCGA-CC-A7IK TCGA-DD-A1EL TCGA-DD-AACT TCGA-DD-AADN 
       13.02        14.76         8.61        13.64        51.35        29.52 
TCGA-DD-AAE3 TCGA-DD-AAVV TCGA-ED-A82E TCGA-G3-A25T TCGA-G3-A5SM TCGA-G3-AAV1 
       18.61        80.71        13.41        51.06        17.10        11.80 
TCGA-KR-A7K2 TCGA-MR-A8JO TCGA-YA-A8S7 
       21.60        10.85        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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        38.40        20.81        22.92 
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 
       17.10         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        23.38 
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        45.93         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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.39         4.24         3.35         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL 
       21.34         9.83        12.00        13.12        12.56         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        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-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-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-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-AACW TCGA-DD-AACX 
       14.20        59.31        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-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       34.49        20.91         0.39        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-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-AAEE 
       21.83        23.74        18.90        15.72        25.08        26.63 
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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         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-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-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-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       22.06        14.70        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.78        15.65        12.23        13.55         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       31.27        29.79        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        22.95        24.56        20.71         7.53        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       26.27        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        36.10         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-AA44 TCGA-WX-AA46 
       10.32        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       18.28        22.78        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        25.15        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              8.61               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             80.71             120.82 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             14.76              19.99 
[1] "8.6 - 80.7 (14.8)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED         5        3         0          5          1
  16Q GAIN WILD-TYPE     166       82         3         55          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                166
  STAGE II                  3                 82
  STAGE III                 0                  3
  STAGE IIIA                5                 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
  16Q GAIN MUTATED       5   3   6   1
  16Q GAIN WILD-TYPE   177  89  68  11
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                5                177
  T2                   3                 89
  T3                   6                 68
  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    12   0
  16Q GAIN WILD-TYPE 238   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     12    0
  16Q GAIN WILD-TYPE  238    3
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               12                238
  1                0                  3
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    11   0
  16Q GAIN WILD-TYPE 250   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     11    0
  16Q GAIN WILD-TYPE  250    4
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               11                250
  1                0                  4
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     4  11
  16Q GAIN WILD-TYPE 111 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4   11
  16Q GAIN WILD-TYPE  111  236
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                4                111
  MALE                 11                236
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    14   1
  16Q GAIN WILD-TYPE 322   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     14    1
  16Q GAIN WILD-TYPE  322    6
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                14                322
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16Q GAIN MUTATED                         1                       13
  16Q GAIN WILD-TYPE                       1                      340
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16Q GAIN MUTATED                                  1
  16Q GAIN WILD-TYPE                                6
D29V9, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       13                340
  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    13   0   0   2
  16Q GAIN WILD-TYPE 305  15   1  19
D29V10, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               13                305
  R1                0                 15
  R2                0                  1
  RX                2                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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     7
  16Q GAIN WILD-TYPE                                1   150
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           2     6
  16Q GAIN WILD-TYPE                        15   171
D29V11, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                150
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                           6                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"
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  12
  16Q GAIN WILD-TYPE  12 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   12
  16Q GAIN WILD-TYPE   12  320
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               12                320
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    19  11
  17P GAIN WILD-TYPE 210 118
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                30                328 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                11                118 
$`17P GAIN MUTATED`
TCGA-3K-AAZ8 TCGA-BC-A10Q TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-CC-A7IE TCGA-CC-A7IG 
       13.02        37.32         0.66         9.86         7.13         9.83 
TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A3A7 TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73D 
        8.15        37.78        13.78        73.81       108.76        22.78 
TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AACS TCGA-DD-AAD0 TCGA-DD-AAD5 
       11.41        76.41        53.19        59.31         4.50        44.22 
TCGA-DD-AADD TCGA-DD-AAE3 TCGA-ED-A66X TCGA-ED-A66Y TCGA-EP-A2KB TCGA-ES-A2HS 
       40.47        18.61        13.35         9.73        19.59        22.85 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-AAV6 TCGA-NI-A8LF TCGA-UB-A7MA TCGA-UB-AA0U 
       81.73        30.74         2.14        26.27        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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        38.40        20.81        22.92 
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 
       17.10        14.76         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        23.38 
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        45.93         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         4.24         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.35         3.32         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II 
       11.41         9.99         8.94        21.34        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.56         8.61         9.14         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        6.94        79.73        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-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-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA 
        1.45        35.67       114.35        13.48         0.53        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-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-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59        47.67         5.62        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-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-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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       26.93        28.08        13.91         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-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-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-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        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-A7M5 TCGA-G3-A7M6 
       22.95        20.42        17.10        22.06        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       11.87        14.14         1.84        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       12.23        13.55         0.89         8.75        11.87        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83        11.80         2.14        21.60        31.27        29.79 
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        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       24.56        20.71         7.53        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        36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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        35.87         0.69        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.66               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            108.76             120.82 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            19.100             19.775 
[1] "0.7 - 108.8 (19.1)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
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     159       79         3         52          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                159
  STAGE II                  6                 79
  STAGE III                 0                  3
  STAGE IIIA                8                 52
  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   170  85  63  12
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1               12                170
  T2                   7                 85
  T3                  11                 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"
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    20   0
  17P GAIN WILD-TYPE 230   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     20    0
  17P GAIN WILD-TYPE  230    3
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               20                230
  1                0                  3
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    22   0
  17P GAIN WILD-TYPE 239   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     22    0
  17P GAIN WILD-TYPE  239    4
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               22                239
  1                0                  4
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     9  21
  17P GAIN WILD-TYPE 106 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      9   21
  17P GAIN WILD-TYPE  106  226
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                9                106
  MALE                 21                226
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    29   0
  17P GAIN WILD-TYPE 307   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     29    0
  17P GAIN WILD-TYPE  307    7
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                29                307
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17P GAIN MUTATED                         0                       29
  17P GAIN WILD-TYPE                       2                      324
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17P GAIN MUTATED                                  1
  17P GAIN WILD-TYPE                                6
D30V9, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       29                324
  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 294  11   1  19
D30V10, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               24                294
  R1                4                 11
  R2                0                  1
  RX                2                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   143
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           3    12
  17P GAIN WILD-TYPE                        14   165
D30V11, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          14                143
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          12                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"
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  29
  17P GAIN WILD-TYPE  13 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   29
  17P GAIN WILD-TYPE   13  303
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               29                303
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    58  34
  17Q GAIN WILD-TYPE 171  95
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                92                266 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                34                 95 
$`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        22.92        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        23.38         1.12         5.03 
TCGA-BC-A217 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       45.93        14.60         0.66         2.86         3.19         4.24 
TCGA-CC-5264 TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        3.35        11.93        11.41         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IK TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A 
        9.83         8.61         8.15        37.78         7.33         2.60 
TCGA-DD-A1EA TCGA-DD-A1EI TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A9 
       79.40         6.02         5.62        17.59        13.78        30.61 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC9 TCGA-DD-AACA 
       73.81       108.76        22.78         1.45        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACS TCGA-DD-AACX 
       76.41        63.48        53.19        69.11        59.31         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD5 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG 
        4.50        44.22        13.97        40.47        39.52        37.64 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAEA TCGA-DD-AAEE 
       14.89        66.67        18.21        18.61        18.90        26.63 
TCGA-DD-AAVV TCGA-DD-AAW1 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A8O6 
       80.71        65.39        13.35         9.73         0.20         1.84 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25U 
       19.59         0.62        22.85         0.03        81.73        53.79 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-AAUZ 
       30.74        21.53        19.23        22.95        20.78        15.78 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
        8.75         2.14        22.95        20.71        26.27        17.69 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-AA0U TCGA-WJ-A86L TCGA-ZP-A9CZ 
       17.59        19.76        16.44        10.75        11.34        23.21 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.15        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        49.84        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG 
       38.40        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        17.10        14.76        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         4.24         3.39         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        9.96        10.36         9.99        12.00        13.12        12.56 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 
        9.14         4.60        11.31         9.17         6.94        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57        53.33       113.00         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       90.71        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        55.69        19.76        25.81         7.66        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       90.28        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       56.25        29.56        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.93         9.30        23.05        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
        0.53        55.40        12.53        12.00        15.42         6.41 
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-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY 
       14.20        51.35        51.52        50.33        46.82        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-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.54        40.83         3.78        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
       20.91         0.39        29.52        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-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
       19.99         4.64        21.17        21.83        23.74        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-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-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       64.77        62.47        66.25        49.48        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       26.93        28.08        13.91         0.20        12.82        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-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       20.61         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-A496 
       19.10        27.88         8.12         6.38        12.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        13.68        51.06        28.27        58.49        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL 
       22.13        25.64         5.92        19.53        25.25        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       17.10        22.06        14.70        11.87        14.14         1.84 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
       15.65        11.80        12.23        13.55         0.89        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83        11.80         2.14        21.60        31.27 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       29.79        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 
       24.56         7.53        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        36.10 
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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 
       12.99        20.22        24.85        18.28        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       35.77        25.71        35.87         0.69        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.03               0.20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            120.82             114.35 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             18.41              20.17 
[1] "0.0 - 120.8 (18.4)" "0.2 - 114.3 (20.2)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED        38       21         0         19          4
  17Q GAIN WILD-TYPE     133       64         3         41          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                133
  STAGE II                 21                 64
  STAGE III                 0                  3
  STAGE IIIA               19                 41
  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  24  24   5
  17Q GAIN WILD-TYPE   142  68  50   7
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1               40                142
  T2                  24                 68
  T3                  24                 50
  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    63   0
  17Q GAIN WILD-TYPE 187   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     63    0
  17Q GAIN WILD-TYPE  187    3
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               63                187
  1                0                  3
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    65   2
  17Q GAIN WILD-TYPE 196   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     65    2
  17Q GAIN WILD-TYPE  196    2
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               65                196
  1                2                  2
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    23  70
  17Q GAIN WILD-TYPE  92 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     23   70
  17Q GAIN WILD-TYPE   92  177
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               23                 92
  MALE                 70                177
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    84   1
  17Q GAIN WILD-TYPE 252   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     84    1
  17Q GAIN WILD-TYPE  252    6
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                84                252
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17Q GAIN MUTATED                         0                       92
  17Q GAIN WILD-TYPE                       2                      261
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17Q GAIN MUTATED                                  1
  17Q GAIN WILD-TYPE                                6
D31V9, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       92                261
  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    78   7   1   7
  17Q GAIN WILD-TYPE 240   8   0  14
D31V10, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               78                240
  R1                7                  8
  R2                1                  0
  RX                7                 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
  17Q GAIN MUTATED                                  0    48
  17Q GAIN WILD-TYPE                                1   109
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           6    36
  17Q GAIN WILD-TYPE                        11   141
D31V11, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          48                109
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          36                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"
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     3  88
  17Q GAIN WILD-TYPE  10 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3   88
  17Q GAIN WILD-TYPE   10  244
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               88                244
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    24  11
  18P GAIN WILD-TYPE 205 118
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                35                323 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                11                118 
$`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        38.40        13.02         0.66 
TCGA-CC-5263 TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ 
        4.24        11.93        11.41         9.83        13.12        12.56 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN TCGA-DD-AACF 
        6.94         8.15        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        36.10         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        49.84        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        22.92         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        17.10        14.76         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        23.38         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        45.93         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         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.19         3.39         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        9.96        10.36         9.99         8.94         7.13        21.34 
TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.00         8.61         9.14         4.60        11.31         9.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        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-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-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        39.78        56.25        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-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-AADB TCGA-DD-AADE TCGA-DD-AADG 
       22.09        40.08        40.54        40.83        39.52        37.64 
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-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       15.06        14.33        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-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-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVQ 
       26.63        23.64        25.78        50.33        35.08        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        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 
       29.92        26.93        28.08        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        22.06 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       14.70        20.78        11.87        14.14         1.84        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       21.60        31.27        29.79        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        22.95        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA 
       21.04        19.33        19.04        15.52         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.32        11.34        12.99        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       22.78        13.55        35.77        25.71        35.87        25.15 
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 
              0.66               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             81.73             120.82 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             13.97              19.79 
[1] "0.7 - 81.7 (14.0)"  "0.0 - 120.8 (19.8)"
[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     159       77         3         51          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                159
  STAGE II                  8                 77
  STAGE III                 0                  3
  STAGE IIIA                9                 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
  18P GAIN MUTATED      14   9  12   0
  18P GAIN WILD-TYPE   168  83  62  12
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1               14                168
  T2                   9                 83
  T3                  12                 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"
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    26   0
  18P GAIN WILD-TYPE 224   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     26    0
  18P GAIN WILD-TYPE  224    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               26                224
  1                0                  3
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    25   1
  18P GAIN WILD-TYPE 236   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     25    1
  18P GAIN WILD-TYPE  236    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               25                236
  1                1                  3
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    10  25
  18P GAIN WILD-TYPE 105 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     10   25
  18P GAIN WILD-TYPE  105  222
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               10                105
  MALE                 25                222
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    34   0
  18P GAIN WILD-TYPE 302   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     34    0
  18P GAIN WILD-TYPE  302    7
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                34                302
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18P GAIN MUTATED                         0                       35
  18P GAIN WILD-TYPE                       2                      318
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18P GAIN MUTATED                                  0
  18P GAIN WILD-TYPE                                7
D32V9, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       35                318
  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 289  14   0  18
D32V10, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               29                289
  R1                1                 14
  R2                1                  0
  RX                3                 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
  18P GAIN MUTATED                                  0    21
  18P GAIN WILD-TYPE                                1   136
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           3    11
  18P GAIN WILD-TYPE                        14   166
D32V11, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          21                136
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          11                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"
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1  34
  18P GAIN WILD-TYPE  12 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   34
  18P GAIN WILD-TYPE   12  298
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               34                298
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    17  10
  18Q GAIN WILD-TYPE 212 119
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                27                331 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                119 
$`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-CC-A5UC TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A9FW 
       11.93        11.41         9.83        13.12        12.56         8.15 
TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN TCGA-DD-AACF TCGA-DD-AADC TCGA-DD-AADD 
       79.73         7.33        29.56        12.00        13.97        40.47 
TCGA-DD-AADJ TCGA-DD-AADR TCGA-DD-AAE3 TCGA-EP-A3JL TCGA-FV-A4ZP TCGA-G3-A25T 
       35.05        66.67        18.61         9.96        81.73        51.06 
TCGA-G3-A25X TCGA-RC-A7SH TCGA-ZP-A9D1 
       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        49.84        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I 
       38.40        20.81        22.92         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        17.10        14.76         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        23.38         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        45.93         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-5264 TCGA-CC-A1HT 
        4.24         2.86         3.19         3.39         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
        9.86         9.96        10.36         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       21.34        12.00         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        9.17         6.94        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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        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-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        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-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39        13.68        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-A7M5 
       25.25        22.95        20.42        17.10        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        22.92         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83        11.80         2.14        21.60 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       31.27        29.79        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        22.95        24.56        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.33        19.04        15.52        36.10         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-AA44 TCGA-WX-AA46 
       10.32        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       18.28        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.87        25.15        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.66               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             81.73             120.82 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             13.97              19.99 
[1] "0.7 - 81.7 (14.0)"  "0.0 - 120.8 (20.0)"
[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     162       79         3         52          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                162
  STAGE II                  6                 79
  STAGE III                 0                  3
  STAGE IIIA                8                 52
  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   172  85  64  12
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1               10                172
  T2                   7                 85
  T3                  10                 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"
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    20   0
  18Q GAIN WILD-TYPE 230   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     20    0
  18Q GAIN WILD-TYPE  230    3
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               20                230
  1                0                  3
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    19   1
  18Q GAIN WILD-TYPE 242   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     19    1
  18Q GAIN WILD-TYPE  242    3
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               19                242
  1                1                  3
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     7  20
  18Q GAIN WILD-TYPE 108 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7   20
  18Q GAIN WILD-TYPE  108  227
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                7                108
  MALE                 20                227
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    26   0
  18Q GAIN WILD-TYPE 310   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     26    0
  18Q GAIN WILD-TYPE  310    7
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                26                310
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18Q GAIN MUTATED                         0                       27
  18Q GAIN WILD-TYPE                       2                      326
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18Q GAIN MUTATED                                  0
  18Q GAIN WILD-TYPE                                7
D33V9, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       27                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
  18Q GAIN MUTATED    21   1   1   3
  18Q GAIN WILD-TYPE 297  14   0  18
D33V10, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               21                297
  R1                1                 14
  R2                1                  0
  RX                3                 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
  18Q GAIN MUTATED                                  0    16
  18Q GAIN WILD-TYPE                                1   141
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           2     9
  18Q GAIN WILD-TYPE                        15   168
D33V11, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          16                141
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                           9                168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1  26
  18Q GAIN WILD-TYPE  12 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   26
  18Q GAIN WILD-TYPE   12  306
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               26                306
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    34  19
  19P GAIN WILD-TYPE 195 110
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                53                305 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                19                110 
$`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-CC-A7II TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 
        3.19        13.12        79.73       113.00         7.33        90.71 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A7 TCGA-DD-A3A9 
       19.79        12.95        21.14        55.69        13.78        30.61 
TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73G 
       90.28        29.56        73.81        12.26        78.84       114.35 
TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AAE0 TCGA-DD-AAE3 
       51.35        46.82        40.83         3.78        18.25        18.61 
TCGA-DD-AAEK TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KB 
       35.08         9.73         0.20        14.04        13.41        19.59 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A25T 
        0.62        22.85        60.89        23.97        27.88        51.06 
TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-GJ-A3OU TCGA-KR-A7K2 
       58.49        17.10        11.87        15.65        22.92        21.60 
TCGA-MI-A75G TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-YA-A8S7 TCGA-ZP-A9D1 
       22.95        21.04        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        49.84        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        38.40        20.81        22.92         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        17.10        14.76 
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        23.38         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        45.93         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         4.24 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.39         4.24         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.96        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK 
        7.13        21.34         9.83        12.00        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.14         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       37.78        83.57        53.33         2.60         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-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-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11         0.36        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
      108.76         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-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-AACU TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       51.52        50.33         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-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-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-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        23.64        25.78        50.33        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        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 
       29.92        26.93        28.08        13.91        13.35         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       12.82        13.15        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       19.99        20.61         9.96        11.93        14.40        19.10 
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-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39        13.68        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-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 
       25.25        22.95        20.42        22.06        14.70        20.78 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14         1.84        15.78        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75         2.14        11.87         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        31.27        29.79        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        24.56        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB 
       58.88        26.27        17.69        21.01         3.09        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.52        36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       22.78        35.77        25.71        23.21        35.87        25.15 
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 

  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 
             21.14              19.33 
[1] "0.2 - 114.3 (21.1)" "0.0 - 120.8 (19.3)"
[1] "hr=" "1.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P GAIN MUTATED        24       13         0          9          2
  19P GAIN WILD-TYPE     147       72         3         51          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                  24                147
  STAGE II                 13                 72
  STAGE III                 0                  3
  STAGE IIIA                9                 51
  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      26  15  12   1
  19P GAIN WILD-TYPE   156  77  62  11
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1               26                156
  T2                  15                 77
  T3                  12                 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"
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    38   1
  19P GAIN WILD-TYPE 212   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     38    1
  19P GAIN WILD-TYPE  212    2
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               38                212
  1                1                  2
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    38   3
  19P GAIN WILD-TYPE 223   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     38    3
  19P GAIN WILD-TYPE  223    1
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               38                223
  1                3                  1
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    24  30
  19P GAIN WILD-TYPE  91 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     24   30
  19P GAIN WILD-TYPE   91  217
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               24                 91
  MALE                 30                217
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    49   1
  19P GAIN WILD-TYPE 287   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     49    1
  19P GAIN WILD-TYPE  287    6
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                49                287
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19P GAIN MUTATED                         0                       52
  19P GAIN WILD-TYPE                       2                      301
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19P GAIN MUTATED                                  2
  19P GAIN WILD-TYPE                                5
D34V9, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       52                301
  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   5
  19P GAIN WILD-TYPE 271  14   0  16
D34V10, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               47                271
  R1                1                 14
  R2                1                  0
  RX                5                 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
  19P GAIN MUTATED                                  0    18
  19P GAIN WILD-TYPE                                1   139
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           4    31
  19P GAIN WILD-TYPE                        13   146
D34V11, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          18                139
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          31                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"
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  49
  19P GAIN WILD-TYPE  10 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   49
  19P GAIN WILD-TYPE   10  283
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               49                283
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    45  24
  19Q GAIN WILD-TYPE 184 105
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                69                289 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                24                105 
$`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        49.84        13.02        37.32        10.13 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A7II TCGA-DD-A113 
       13.45         0.66         3.19         9.86        13.12        79.73 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG 
      113.00         7.33        90.71        19.79        12.95        45.11 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO 
       21.14        55.69        30.61        90.28        29.56        73.81 
TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACO TCGA-DD-AACP 
       12.26        78.84       114.35        15.42        61.68        13.64 
TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       51.35        46.82        40.83        13.97        40.47         3.78 
TCGA-DD-AADM TCGA-DD-AAE0 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEK TCGA-DD-AAVV 
        0.39        18.25        21.17        18.90        35.08        80.71 
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-FV-A4ZQ TCGA-G3-A25T 
       22.85        60.89        23.97        27.88         0.39        51.06 
TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-GJ-A3OU 
       58.49        17.10        20.78        11.87        15.65        22.92 
TCGA-KR-A7K2 TCGA-MI-A75G TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7ME 
       21.60        22.95        26.27        21.04        15.39        15.98 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 
       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 
       38.40        20.81        22.92         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        17.10        14.76         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        23.38         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 
       45.93         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         4.24         2.86         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.35         3.32         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       12.00        12.56         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        9.17         6.94         8.15        37.78        83.57        53.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        21.76        51.29        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        11.47        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-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
        0.36        33.14        32.52        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       30.51        39.78        56.25       108.76         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
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-AACI TCGA-DD-AACJ 
       12.53        63.48        12.00         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACS 
        0.30         3.52        58.16        42.81        14.20        59.31 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       51.52        50.33         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-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.54        39.52        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91        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-AAE8 TCGA-DD-AAE9 
       20.98        18.61        19.99         4.64        21.83        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        26.63        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        29.92        26.93        28.08        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-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
       81.73        13.68        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-A6UC TCGA-G3-A7M5 TCGA-G3-A7M8 
       25.25        22.95        20.42        22.06        14.70        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        15.78        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14        11.87         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       31.27        29.79        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        24.56        20.71         7.53        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 
       36.10         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-AA44 
        7.04        10.75        10.32        11.34         0.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       24.85        18.28        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.87        25.15        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.20               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            114.35             120.82 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             21.04              19.33 
[1] "0.2 - 114.3 (21.0)" "0.0 - 120.8 (19.3)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED        34       18         0         10          1
  19Q GAIN WILD-TYPE     137       67         3         50          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                  34                137
  STAGE II                 18                 67
  STAGE III                 0                  3
  STAGE IIIA               10                 50
  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      36  20  13   1
  19Q GAIN WILD-TYPE   146  72  61  11
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1               36                146
  T2                  20                 72
  T3                  13                 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"
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    47   1
  19Q GAIN WILD-TYPE 203   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     47    1
  19Q GAIN WILD-TYPE  203    2
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               47                203
  1                1                  2
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    49   3
  19Q GAIN WILD-TYPE 212   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     49    3
  19Q GAIN WILD-TYPE  212    1
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               49                212
  1                3                  1
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    26  44
  19Q GAIN WILD-TYPE  89 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     26   44
  19Q GAIN WILD-TYPE   89  203
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               26                 89
  MALE                 44                203
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    64   1
  19Q GAIN WILD-TYPE 272   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     64    1
  19Q GAIN WILD-TYPE  272    6
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                64                272
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19Q GAIN MUTATED                         0                       68
  19Q GAIN WILD-TYPE                       2                      285
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19Q GAIN MUTATED                                  2
  19Q GAIN WILD-TYPE                                5
D35V9, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       68                285
  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    63   1   1   5
  19Q GAIN WILD-TYPE 255  14   0  16
D35V10, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               63                255
  R1                1                 14
  R2                1                  0
  RX                5                 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
  19Q GAIN MUTATED                                  0    28
  19Q GAIN WILD-TYPE                                1   129
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           4    38
  19Q GAIN WILD-TYPE                        13   139
D35V11, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          28                129
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          38                139
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     4  65
  19Q GAIN WILD-TYPE   9 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      4   65
  19Q GAIN WILD-TYPE    9  267
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  9
  NOT HISPANIC OR LATINO               65                267
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    56  49
  20P GAIN WILD-TYPE 173  80
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               105                253 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                49                 80 
$`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        22.92 
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 
       45.93         0.26        14.60        44.81        13.45         0.66 
TCGA-CC-5261 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UE 
        3.19         3.35         9.86        10.36        11.41         8.94 
TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A118 TCGA-DD-A119 
        7.13        13.12        11.31         8.15       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ 
        2.60         0.46        12.95        45.11        49.15        33.04 
TCGA-DD-A39V TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NR 
       21.14        13.78        30.61        90.28        29.56         0.30 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACH 
       78.84       114.35         0.53        76.41        55.40         6.41 
TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACZ 
       53.19        61.68        13.64        51.35        50.33         5.62 
TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN TCGA-DD-AADO 
       22.09        40.47         3.78        37.64        29.52        14.89 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE9 
       15.58        18.21        19.30        18.25        18.61        23.74 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVV TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO 
       25.78        35.08        80.71        13.35         9.73        14.04 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B 
       13.41         1.84        19.59         9.96        22.85        60.89 
TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SM 
        6.38         0.39        13.68        58.49        14.86        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 
       22.06        20.78         1.84        11.80         0.89         2.14 
TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A8LF 
        2.99        21.60        31.27        12.72        22.95        26.27 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       36.10        17.59        19.76        10.75         0.99        12.99 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD 
       22.78        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        49.84        47.74        18.25        11.74        38.40 
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        17.10 
TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       14.76        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        23.38         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         4.24 
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         9.96        11.93 
TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK 
        9.99        21.34         9.83        12.00        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 
        9.14         4.60         9.17         6.94        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       83.57        53.33        21.76        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-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       12.00        15.42        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       42.81        14.20        59.31        51.52        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-AADE TCGA-DD-AADI 
       40.08        40.54        40.83        13.97        39.52        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ 
       35.05        34.49        20.91         0.39        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       66.67        18.87        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-AAVR 
       26.63        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-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       28.08        13.91         0.20        12.82         0.20        13.15 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       13.35         0.20        18.74        19.99        20.61         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       11.93        14.40        23.97        19.10        27.88         8.12 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U 
       12.03         0.03         0.33        81.73        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-A7M5 
       19.53        19.23        25.25        22.95        20.42        14.70 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       11.87        14.14        15.78        15.65        12.23        13.55 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 
        8.75        11.87        22.92         1.02         2.20        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 
       20.75        17.06        16.83        11.80         2.14        29.79 
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        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
        7.53        10.85        58.88        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 
       21.04        19.33        19.04        15.39        15.52         0.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       16.44         1.71        15.98         7.04        10.32        11.34 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       20.22        24.85        18.28        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.87         0.69        25.15        12.99        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.26               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            114.35             120.82 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             17.59              20.42 
[1] "0.3 - 114.3 (17.6)" "0.0 - 120.8 (20.4)"
[1] "hr=" "1.7"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED        43       27         1         22          4
  20P GAIN WILD-TYPE     128       58         2         38          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                  43                128
  STAGE II                 27                 58
  STAGE III                 1                  2
  STAGE IIIA               22                 38
  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      45  30  29   3
  20P GAIN WILD-TYPE   137  62  45   9
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               45                137
  T2                  30                 62
  T3                  29                 45
  T4                   3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    74   1
  20P GAIN WILD-TYPE 176   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     74    1
  20P GAIN WILD-TYPE  176    2
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               74                176
  1                1                  2
[1] 2 2
[1] FALSE
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    80   3
  20P GAIN WILD-TYPE 181   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     80    3
  20P GAIN WILD-TYPE  181    1
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               80                181
  1                3                  1
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    39  68
  20P GAIN WILD-TYPE  76 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     39   68
  20P GAIN WILD-TYPE   76  179
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               39                 76
  MALE                 68                179
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    98   1
  20P GAIN WILD-TYPE 238   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     98    1
  20P GAIN WILD-TYPE  238    6
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                98                238
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20P GAIN MUTATED                         0                      105
  20P GAIN WILD-TYPE                       2                      248
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20P GAIN MUTATED                                  2
  20P GAIN WILD-TYPE                                5
D36V9, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                      105                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
  20P GAIN MUTATED    94   6   1   5
  20P GAIN WILD-TYPE 224   9   0  16
D36V10, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               94                224
  R1                6                  9
  R2                1                  0
  RX                5                 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
  20P GAIN MUTATED                                  0    45
  20P GAIN WILD-TYPE                                1   112
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           4    56
  20P GAIN WILD-TYPE                        13   121
D36V11, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          45                112
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          56                121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     4  96
  20P GAIN WILD-TYPE   9 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4   96
  20P GAIN WILD-TYPE    9  236
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  9
  NOT HISPANIC OR LATINO               96                236
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    62  48
  20Q GAIN WILD-TYPE 167  81
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               110                248 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                48                 81 
$`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        22.92 
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 
       45.93         0.26        14.60        44.81        13.45         0.66 
TCGA-CC-5261 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.19         3.35         9.86        10.36        11.93        11.41 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FW 
        8.94         7.13        13.12         9.14        11.31         8.15 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF 
      113.00         7.33         2.60         0.46        21.76        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A7 TCGA-DD-A3A9 
       45.11        49.15        33.04        21.14        13.78        30.61 
TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC8 
       90.28        29.56         0.30        78.84       114.35         0.53 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS 
       76.41        55.40        53.19        61.68        13.64        59.31 
TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADD 
       51.35        50.33         5.62         4.50        22.09        40.47 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU 
        3.78        37.64        29.52        14.89        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEH 
       19.30        18.25        18.61        23.74        18.90        25.78 
TCGA-DD-AAEK TCGA-DD-AAVV TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A82E 
       35.08        80.71        13.35         9.73        14.04        13.41 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 
        1.84        19.59         9.96        22.85        60.89         6.38 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
        0.39        13.68        58.49        17.10        22.06        20.78 
TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.84        11.80         2.14         2.99        21.60        31.27 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RG-A7D4 TCGA-UB-A7MA 
       12.72        22.95        26.27        21.01        36.10        17.59 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-XR-A8TF 
       19.76        15.98        10.75         0.99        12.99        22.78 
TCGA-YA-A8S7 TCGA-ZS-A9CD 
       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        49.84        47.74        18.25        11.74        38.40 
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        17.10 
TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       14.76        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        23.38         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         4.24 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A5UD 
        2.86         3.39         4.24         3.32         9.96         9.99 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT 
       21.34         9.83        12.00        12.56         8.61         4.60 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        9.17         6.94        79.73        37.78        83.57        53.33 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X 
       11.47         6.02        18.35        13.64        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-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11         0.36        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       73.81       108.76        12.26        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 
       23.05        22.78         1.45        35.67        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       75.65        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-AACQ 
       69.11         0.30         3.52        58.16        42.81        14.20 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD1 TCGA-DD-AAD2 
       51.52        46.82         5.59        47.67        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-AAEB 
       20.98        19.99         4.64        21.17        21.83        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        26.63        23.64        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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       26.93        28.08        13.91         0.20        12.82         0.20 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.15        13.35         0.20        18.74        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
        0.62        11.93        14.40        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T 
        8.12        12.03         0.03         0.33        81.73        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.42        14.70        11.87        14.14        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       12.23        13.55         0.89         8.75        11.87        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80         2.14        29.79        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        24.56        20.71         7.53        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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34        20.22        24.85        18.28        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE 
       23.21        35.87         0.69        25.15        12.99        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.26               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            114.35             120.82 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             18.23              20.32 
[1] "0.3 - 114.3 (18.2)" "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        46       26         1         24          5
  20Q GAIN WILD-TYPE     125       59         2         36          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                  46                125
  STAGE II                 26                 59
  STAGE III                 1                  2
  STAGE IIIA               24                 36
  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      48  28  31   4
  20Q GAIN WILD-TYPE   134  64  43   8
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               48                134
  T2                  28                 64
  T3                  31                 43
  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    77   1
  20Q GAIN WILD-TYPE 173   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     77    1
  20Q GAIN WILD-TYPE  173    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               77                173
  1                1                  2
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    84   2
  20Q GAIN WILD-TYPE 177   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     84    2
  20Q GAIN WILD-TYPE  177    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               84                177
  1                2                  2
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    38  73
  20Q GAIN WILD-TYPE  77 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     38   73
  20Q GAIN WILD-TYPE   77  174
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               38                 77
  MALE                 73                174
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   102   1
  20Q GAIN WILD-TYPE 234   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    102    1
  20Q GAIN WILD-TYPE  234    6
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               102                234
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20Q GAIN MUTATED                         0                      109
  20Q GAIN WILD-TYPE                       2                      244
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20Q GAIN MUTATED                                  2
  20Q GAIN WILD-TYPE                                5
D37V9, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                      109                244
  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    97   6   1   5
  20Q GAIN WILD-TYPE 221   9   0  16
D37V10, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               97                221
  R1                6                  9
  R2                1                  0
  RX                5                 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
  20Q GAIN MUTATED                                  0    49
  20Q GAIN WILD-TYPE                                1   108
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           4    56
  20Q GAIN WILD-TYPE                        13   121
D37V11, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          49                108
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          56                121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3 101
  20Q GAIN WILD-TYPE  10 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  101
  20Q GAIN WILD-TYPE   10  231
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO              101                231
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    14  11
  21Q GAIN WILD-TYPE 215 118
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                25                333 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                11                118 
$`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        45.93         0.66 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IG TCGA-DD-A113 
        3.19         4.24        11.41         7.13         9.83        79.73 
TCGA-DD-A3A5 TCGA-DD-A4NV TCGA-DD-AAEK TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS 
      102.74        78.84        35.08        13.41        19.59        22.85 
TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A3CG TCGA-G3-AAUZ TCGA-MI-A75G TCGA-RC-A7SH 
       27.88        51.06        22.13        15.78        22.95        15.39 
TCGA-UB-AA0U 
       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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       18.25        11.74        38.40        22.92         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        17.10        14.76         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        23.38         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         4.24 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.39         3.35         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IH 
       10.36        11.93         9.99         8.94        21.34        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       13.12        12.56         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        9.17         6.94         8.15        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-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       25.81         7.66        70.06        17.59        20.12       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        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-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-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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        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-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-A3I1 TCGA-FV-A3R2 
       14.40        60.89        23.97        19.10         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
       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-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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       20.42        17.10        22.06        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14         1.84        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89         8.75         2.14        11.87        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       11.80         2.14        21.60        31.27        29.79        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        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        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        36.10 
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-AA44 
        7.04        10.32        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       24.85        18.28        22.78        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        35.87         0.69        25.15        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       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 
             19.59              19.76 
[1] "0.7 - 102.7 (19.6)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
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     166       73         2         53          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                166
  STAGE II                 12                 73
  STAGE III                 1                  2
  STAGE IIIA                7                 53
  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   176  81  65  12
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                6                176
  T2                  11                 81
  T3                   9                 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"
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    16   0
  21Q GAIN WILD-TYPE 234   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     16    0
  21Q GAIN WILD-TYPE  234    3
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               16                234
  1                0                  3
[1] 2 2
[1] FALSE
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    18   0
  21Q GAIN WILD-TYPE 243   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     18    0
  21Q GAIN WILD-TYPE  243    4
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               18                243
  1                0                  4
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     9  17
  21Q GAIN WILD-TYPE 106 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9   17
  21Q GAIN WILD-TYPE  106  230
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                9                106
  MALE                 17                230
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    24   0
  21Q GAIN WILD-TYPE 312   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     24    0
  21Q GAIN WILD-TYPE  312    7
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                24                312
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  21Q GAIN MUTATED                         0                       25
  21Q GAIN WILD-TYPE                       2                      328
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  21Q GAIN MUTATED                                  1
  21Q GAIN WILD-TYPE                                6
D38V9, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       25                328
  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 299  13   1  16
D38V10, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               19                299
  R1                2                 13
  R2                0                  1
  RX                5                 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
  21Q GAIN MUTATED                                  0     8
  21Q GAIN WILD-TYPE                                1   149
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           2    15
  21Q GAIN WILD-TYPE                        15   162
D38V11, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                149
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          15                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"
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  24
  21Q GAIN WILD-TYPE  12 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   24
  21Q GAIN WILD-TYPE   12  308
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               24                308
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    28  19
  22Q GAIN WILD-TYPE 201 110
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                47                311 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                110 
$`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         4.24         3.19 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IL 
       10.36        11.41         8.94         9.83        12.56         9.14 
TCGA-CC-A9FW TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1EJ TCGA-DD-A4ND TCGA-DD-A73G 
        8.15       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        20.78        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        49.84        47.74        18.25        11.74        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
       20.81        22.92         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        17.10        14.76         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 
       23.38         1.12        69.57        44.42        45.93         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-5264 TCGA-CC-A1HT 
       36.66         2.86         3.39         4.24         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF 
        9.86         9.96        11.93         9.99         7.13        21.34 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.00        13.12         8.61         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        6.94        79.73        37.78        83.57        53.33         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        21.76        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
        6.02        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-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        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-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-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-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-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-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       18.90        15.72        26.63        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       79.07        89.69        82.62        59.93        72.39        80.71 
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        29.92        26.93        28.08        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-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        22.06        14.70        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        15.78        15.65        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        8.75         2.14        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        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-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
       36.10         0.76        19.76        16.44         1.71         7.04 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.32        11.34        12.99        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       22.78        35.77        25.71        23.21        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       25.15        12.99        45.57        40.80        79.30 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.20               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            114.35             120.82 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             14.60              20.12 
[1] "0.2 - 114.3 (14.6)" "0.0 - 120.8 (20.1)"
[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     159       68         3         48          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                159
  STAGE II                 17                 68
  STAGE III                 0                  3
  STAGE IIIA               12                 48
  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   169  75  58  10
D39V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1               13                169
  T2                  17                 75
  T3                  16                 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"
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    30   1
  22Q GAIN WILD-TYPE 220   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     30    1
  22Q GAIN WILD-TYPE  220    2
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               30                220
  1                1                  2
[1] 2 2
[1] FALSE
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    33   0
  22Q GAIN WILD-TYPE 228   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     33    0
  22Q GAIN WILD-TYPE  228    4
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               33                228
  1                0                  4
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    19  29
  22Q GAIN WILD-TYPE  96 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     19   29
  22Q GAIN WILD-TYPE   96  218
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               19                 96
  MALE                 29                218
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    46   0
  22Q GAIN WILD-TYPE 290   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     46    0
  22Q GAIN WILD-TYPE  290    7
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                46                290
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  22Q GAIN MUTATED                         0                       46
  22Q GAIN WILD-TYPE                       2                      307
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  22Q GAIN MUTATED                                  2
  22Q GAIN WILD-TYPE                                5
D39V9, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       46                307
  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 278  12   1  16
D39V10, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               40                278
  R1                3                 12
  R2                0                  1
  RX                5                 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
  22Q GAIN MUTATED                                  0    23
  22Q GAIN WILD-TYPE                                1   134
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           2    23
  22Q GAIN WILD-TYPE                        15   154
D39V11, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          23                134
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          23                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"
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  47
  22Q GAIN WILD-TYPE  12 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   47
  22Q GAIN WILD-TYPE   12  285
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               47                285
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    25  16
  XP GAIN WILD-TYPE 204 113
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               41               317 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               16               113 
$`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-CC-A5UC TCGA-CC-A7IJ TCGA-CC-A8HU TCGA-DD-A3A3 TCGA-DD-A3A7 
        2.86        11.41        12.56        11.31        17.59        13.78 
TCGA-DD-A4NK TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AACD TCGA-DD-AACJ 
       39.78        78.84        22.78       114.35        12.53        69.11 
TCGA-DD-AACT TCGA-DD-AAD2 TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAVV 
       51.35        21.63        18.21        18.61        23.74        80.71 
TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A3JL TCGA-FV-A4ZQ 
       64.77        49.48        18.74        20.61         9.96         0.39 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-AAV5 TCGA-LG-A6GG 
       22.13        19.53        25.25        20.42         8.75        12.72 
TCGA-O8-A75V TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-WX-AA47 TCGA-ZS-A9CD 
       17.69        15.98         0.99        18.28        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        49.84        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        38.40        20.81        22.92         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        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
       14.76         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        23.38        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        45.93        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         4.24 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        3.19         3.39         4.24         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
        9.96        10.36        11.93         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL 
       21.34         9.83        12.00        13.12         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
        4.60         9.17         6.94         8.15        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-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-A3A4 
        5.62        19.76        25.81         7.66        70.06        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-A4NL 
       90.28        30.97        30.15        26.83        30.51        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
       23.93         9.30        23.05         1.45        35.67        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE 
        0.53        11.41        75.65        76.41        55.40        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        53.19         0.30         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-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        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-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        26.63        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-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A459 
       56.48        62.47        66.25        65.39        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        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-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
        1.84         0.20        19.99        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-A4ZP 
        8.12         6.38        12.03         0.03         0.33        81.73 
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-A3CK TCGA-G3-A5SJ 
       14.86        21.53        25.64         5.92        19.23        22.95 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       17.10        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         2.14        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        21.60        31.27        29.79        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        22.95        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       10.85        58.88        26.27        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        36.10         0.76 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U 
       17.59        19.76        16.44         1.71         7.04        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-XR-A8TF 
       10.32        11.34        12.99        20.22        24.85        22.78 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        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 
            18.74             19.79 
[1] "0.3 - 114.3 (18.7)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XP GAIN MUTATED        18       11         0          7          1          1
  XP GAIN WILD-TYPE     153       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               153
  STAGE II                11                74
  STAGE III                0                 3
  STAGE IIIA               7                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  12  10   1
  XP GAIN WILD-TYPE   164  80  64  11
D40V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1              18               164
  T2                 12                80
  T3                 10                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    25   0
  XP GAIN WILD-TYPE 225   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     25    0
  XP GAIN WILD-TYPE  225    3
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              25               225
  1               0                 3
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    28   0
  XP GAIN WILD-TYPE 233   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     28    0
  XP GAIN WILD-TYPE  233    4
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              28               233
  1               0                 4
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    13  28
  XP GAIN WILD-TYPE 102 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     13   28
  XP GAIN WILD-TYPE  102  219
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              13               102
  MALE                28               219
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    36   2
  XP GAIN WILD-TYPE 300   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     36    2
  XP GAIN WILD-TYPE  300    5
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               36               300
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XP GAIN MUTATED                         0                       41
  XP GAIN WILD-TYPE                       2                      312
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XP GAIN MUTATED                                  0
  XP GAIN WILD-TYPE                                7
D40V9, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      41               312
  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    36   3   0   1
  XP GAIN WILD-TYPE 282  12   1  20
D40V10, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              36               282
  R1               3                12
  R2               0                 1
  RX               1                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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    17
  XP GAIN WILD-TYPE                                0   140
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                           1    20
  XP GAIN WILD-TYPE                        16   157
D40V11, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         17               140
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         20               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"
D40V12, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     1  38
  XP GAIN WILD-TYPE  12 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1   38
  XP GAIN WILD-TYPE   12  294
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              38               294
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    43  20
  XQ GAIN WILD-TYPE 186 109
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               63               295 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               20               109 
$`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        17.10 
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-CC-5264 TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A8HU 
        3.35        11.41         8.94        12.00        12.56        11.31 
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-AAVV TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 
       79.07        89.69        80.71        64.77        65.39        49.48 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A25U 
       18.74        20.61         9.96        22.85         0.39        53.79 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-AAV3 TCGA-G3-AAV5 
       22.13        19.53        25.25        20.42        13.55         8.75 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75G TCGA-O8-A75V TCGA-UB-A7ME TCGA-WQ-A9G7 
       16.83        12.72        22.95        17.69        15.98         0.99 
TCGA-WX-AA47 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       18.28        45.57        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        49.84        18.25        11.74        38.40        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG 
       22.92         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        14.76         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 
       23.38        69.57         5.03        44.42        45.93        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 
        4.24         3.19         3.39         4.24         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF 
        9.96        10.36        11.93         9.99         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV 
        9.83        13.12         8.61         9.14         4.60         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        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-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-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 
       70.06        20.12       102.74       107.11         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        90.28        30.15        26.83        30.51 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       80.75        23.93         9.30        23.05         1.45        35.67 
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-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-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
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-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        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-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADV 
       29.52        15.06        14.33        66.67        15.58        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-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-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVR 
       26.63        23.64        25.78        50.33        35.08        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        72.39        76.18        56.48        62.47        66.25 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        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-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A2KB 
       13.41        13.35         1.84         0.20        19.99        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        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-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       81.73        13.68        51.06        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ 
       14.86        21.53        25.64         5.92        19.23        22.95 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       17.10        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 
        1.84        15.78        15.65        11.80        12.23         0.89 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        17.06        11.80         2.14        21.60 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       31.27        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       24.56        20.71         7.53        10.85        58.88        26.27 
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-A7MB TCGA-UB-A7MC 
       15.52        36.10         0.76        17.59        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
        1.71         7.04        10.75        10.32        11.34        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       20.22        24.85        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE 
       23.21        35.87         0.69        25.15        12.99        40.80 
TCGA-ZS-A9CF 
       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 
            19.53             19.76 
[1] "0.3 - 114.3 (19.5)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ GAIN MUTATED        31       16         0         11          2          1
  XQ GAIN WILD-TYPE     140       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               140
  STAGE II                16                69
  STAGE III                0                 3
  STAGE IIIA              11                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  17  13   2
  XQ GAIN WILD-TYPE   151  75  61  10
D41V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1              31               151
  T2                 17                75
  T3                 13                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    43   0
  XQ GAIN WILD-TYPE 207   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     43    0
  XQ GAIN WILD-TYPE  207    3
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              43               207
  1               0                 3
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    44   0
  XQ GAIN WILD-TYPE 217   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     44    0
  XQ GAIN WILD-TYPE  217    4
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              44               217
  1               0                 4
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    15  48
  XQ GAIN WILD-TYPE 100 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     15   48
  XQ GAIN WILD-TYPE  100  199
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              15               100
  MALE                48               199
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    55   3
  XQ GAIN WILD-TYPE 281   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     55    3
  XQ GAIN WILD-TYPE  281    4
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               55               281
  YES               3                 4
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XQ GAIN MUTATED                         0                       63
  XQ GAIN WILD-TYPE                       2                      290
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XQ GAIN MUTATED                                  0
  XQ GAIN WILD-TYPE                                7
D41V9, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      63               290
  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    55   3   0   4
  XQ GAIN WILD-TYPE 263  12   1  17
D41V10, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              55               263
  R1               3                12
  R2               0                 1
  RX               4                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
  XQ GAIN MUTATED                                  1    26
  XQ GAIN WILD-TYPE                                0   131
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           4    30
  XQ GAIN WILD-TYPE                        13   147
D41V11, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         26               131
  BLACK OR AFRICAN AMERICAN                      4                13
  WHITE                                         30               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"
D41V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  59
  XQ GAIN WILD-TYPE  12 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   59
  XQ GAIN WILD-TYPE   12  273
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              59               273
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    51  29
  1P LOSS WILD-TYPE 178 100
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               80               278 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               29               100 
$`1P LOSS MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       24.89        49.84        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        45.93        14.60         4.24         3.19 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HV 
       10.36        11.93         9.99        12.56         9.14         9.17 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A1E9 
        8.15        79.73       113.00         7.33         0.46        90.71 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A9 TCGA-DD-A4NH 
       49.15        33.04        55.69         7.66        30.61        30.15 
TCGA-DD-A4NN TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACH TCGA-DD-AACN TCGA-DD-AACP 
       29.56         9.30         0.53         6.41        42.81        13.64 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD1 TCGA-DD-AADA TCGA-DD-AADJ TCGA-DD-AADO 
       51.52        46.82        18.54        40.54        35.05        14.89 
TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVQ 
       19.30        18.25        18.15        18.61        35.08        89.69 
TCGA-DD-AAVS TCGA-DD-AAVZ TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E 
       59.93        62.47        13.35         9.73        12.82        13.41 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 
       13.35         0.20        19.59         0.62        22.85        27.88 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y 
        0.33        81.73        13.68        53.79        58.49        14.86 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-LG-A9QC 
       20.42        17.10        14.70         2.14        21.60        13.97 
TCGA-MI-A75G TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-WQ-A9G7 
       22.95        15.52        36.10         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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-AAPD 
       20.81        22.92         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 
       17.10        14.76         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        23.38 
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-5264 TCGA-CC-A1HT 
        0.66         2.86         3.39         4.24         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        9.86         9.96        11.41         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU 
        9.83        12.00        13.12         8.61         4.60        11.31 
TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11C 
        6.94        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        26.63        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       79.07        82.62        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       64.77        66.25        65.39        49.48        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO 
       26.93        28.08        13.91         0.20         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
       13.15         1.84        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-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-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.23        25.25        22.95        22.06        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       14.14         1.84        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       13.55         0.89         8.75        11.87        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD 
       11.80         2.14        31.27        29.79        12.72        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        24.56        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD 
       19.33        19.04        15.39        17.59        19.76         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA44 
       15.98         7.04        10.75        10.32        11.34        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       24.85        18.28        22.78        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        35.87        25.15        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.20              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           113.00            120.82 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           15.980            20.765 
[1] "0.2 - 113.0 (16.0)" "0.0 - 120.8 (20.8)"
[1] "hr=" "1.1"
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     137       64         2         45          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               137
  STAGE II                21                64
  STAGE III                1                 2
  STAGE IIIA              15                45
  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   145  70  53  11
D42V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1              37               145
  T2                 22                70
  T3                 21                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"
D42V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    57   1
  1P LOSS WILD-TYPE 193   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     57    1
  1P LOSS WILD-TYPE  193    2
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              57               193
  1               1                 2
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    66   3
  1P LOSS WILD-TYPE 195   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     66    3
  1P LOSS WILD-TYPE  195    1
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              66               195
  1               3                 1
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    30  51
  1P LOSS WILD-TYPE  85 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     30   51
  1P LOSS WILD-TYPE   85  196
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              30                85
  MALE                51               196
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    76   0
  1P LOSS WILD-TYPE 260   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     76    0
  1P LOSS WILD-TYPE  260    7
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               76               260
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1P LOSS MUTATED                         0                       78
  1P LOSS WILD-TYPE                       2                      275
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1P LOSS MUTATED                                  3
  1P LOSS WILD-TYPE                                4
D42V9, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      78               275
  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 247  12   0  15
D42V10, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              71               247
  R1               3                12
  R2               1                 0
  RX               6                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
  1P LOSS MUTATED                                  0    39
  1P LOSS WILD-TYPE                                1   118
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           3    38
  1P LOSS WILD-TYPE                        14   139
D42V11, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         39               118
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         38               139
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3  75
  1P LOSS WILD-TYPE  10 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3   75
  1P LOSS WILD-TYPE   10  257
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                10
  NOT HISPANIC OR LATINO              75               257
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    10  12
  1Q LOSS WILD-TYPE 219 117
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               336 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               117 
$`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        45.93         4.24 
TCGA-CC-A3MB TCGA-CC-A7IJ TCGA-DD-A11B TCGA-DD-A1EJ TCGA-DD-A3A1 TCGA-DD-AACH 
       10.36        12.56         0.46        33.04         7.66         6.41 
TCGA-DD-AACW TCGA-DD-AADW TCGA-DD-AAEK TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
       46.82        19.30        35.08        13.41        13.35         0.20 
TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25U TCGA-UB-AA0U 
       22.85        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        49.84        47.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       38.40        20.81        22.92         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        17.10        14.76 
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        23.38         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-5264 TCGA-CC-A1HT 
        2.86         3.19         3.39         4.24         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.86         9.96        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK 
        7.13        21.34         9.83        12.00        13.12         8.61 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.14         4.60        11.31         9.17         6.94         8.15 
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-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60        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-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
        6.02        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76        25.81        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-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-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42        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-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.35        51.52        50.33         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-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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        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-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-A3R2 
       60.89        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       20.42        17.10        22.06        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       14.14         1.84        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89         8.75         2.14        11.87        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83        11.80         2.14        21.60        31.27        29.79 
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        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       24.56        20.71         7.53        10.85        58.88        26.27 
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        36.10         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       16.44         1.71        15.98         7.04        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
        0.99        12.99        20.22        24.85        18.28        22.78 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        79.30        11.21 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.20              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            81.73            120.82 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            15.83             19.89 
[1] "0.2 - 81.7 (15.8)"  "0.0 - 120.8 (19.9)"
[1] "hr=" "1.8"
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     164       78         3         54          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               164
  STAGE II                 7                78
  STAGE III                0                 3
  STAGE IIIA               6                54
  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   174  85  67  12
D43V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               8               174
  T2                  7                85
  T3                  7                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"
D43V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    14   1
  1Q LOSS WILD-TYPE 236   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14    1
  1Q LOSS WILD-TYPE  236    2
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              14               236
  1               1                 2
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    16   0
  1Q LOSS WILD-TYPE 245   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     16    0
  1Q LOSS WILD-TYPE  245    4
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              16               245
  1               0                 4
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     8  14
  1Q LOSS WILD-TYPE 107 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      8   14
  1Q LOSS WILD-TYPE  107  233
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               8               107
  MALE                14               233
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    21   0
  1Q LOSS WILD-TYPE 315   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     21    0
  1Q LOSS WILD-TYPE  315    7
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               21               315
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1Q LOSS MUTATED                         0                       21
  1Q LOSS WILD-TYPE                       2                      332
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1Q LOSS MUTATED                                  1
  1Q LOSS WILD-TYPE                                6
D43V9, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      21               332
  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 300  13   1  19
D43V10, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              18               300
  R1               2                13
  R2               0                 1
  RX               2                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   146
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           0    10
  1Q LOSS WILD-TYPE                        17   167
D43V11, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11               146
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                         10               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"
D43V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  20
  1Q LOSS WILD-TYPE  13 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   20
  1Q LOSS WILD-TYPE   13  312
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                13
  NOT HISPANIC OR LATINO              20               312
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    22   8
  2P LOSS WILD-TYPE 207 121
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               30               328 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8               121 
$`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        23.38         0.26        14.60 
TCGA-BD-A3EP TCGA-CC-A7II TCGA-CC-A7IL TCGA-DD-A11C TCGA-DD-A39Y TCGA-DD-AACE 
       13.45        13.12         9.14        21.76         5.62        63.48 
TCGA-DD-AACU TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADW TCGA-ED-A459 
       51.52        35.67        20.91        29.52        19.30        29.92 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-FV-A3I1 TCGA-G3-A25S TCGA-G3-A5SM 
        9.73         0.20         0.20         8.12        13.68        17.10 
TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-WQ-AB4B 
       11.87         2.20        21.60        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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       47.74        18.25        11.74        38.40        22.92         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        17.10        14.76 
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        45.93        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         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        3.19         3.39         4.24         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.96        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK 
        7.13        21.34         9.83        12.00        12.56         8.61 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        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-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-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-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-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.35        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-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO 
        3.78        37.64        35.05        34.49         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-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        26.63        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-AAVV 
       79.07        89.69        82.62        59.93        72.39        80.71 
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        26.93        28.08        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       12.82        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-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10        27.88         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       81.73         0.39        51.06        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       19.53        19.23        25.25        22.95        20.42        22.06 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       14.70        20.78        11.87        14.14         1.84        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89         8.75 
TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        2.14        22.92         1.02         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83        11.80         2.14        31.27        29.79 
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        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       24.56        20.71         7.53        10.85        58.88        26.27 
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-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        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-A9G7 
       15.98         7.04        10.75        10.32        11.34         0.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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        35.87         0.69        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       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 
           13.565            20.170 
[1] "0.2 - 63.5 (13.6)"  "0.0 - 120.8 (20.2)"
[1] "hr=" "1.1"
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     157       74         3         57          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               157
  STAGE II                11                74
  STAGE III                0                 3
  STAGE IIIA               3                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
  2P LOSS MUTATED      16  10   4   1
  2P LOSS WILD-TYPE   166  82  70  11
D44V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1              16               166
  T2                 10                82
  T3                  4                70
  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 232   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     18    0
  2P LOSS WILD-TYPE  232    3
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              18               232
  1               0                 3
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    24   0
  2P LOSS WILD-TYPE 237   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     24    0
  2P LOSS WILD-TYPE  237    4
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              24               237
  1               0                 4
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7  24
  2P LOSS WILD-TYPE 108 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7   24
  2P LOSS WILD-TYPE  108  223
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7               108
  MALE                24               223
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    27   1
  2P LOSS WILD-TYPE 309   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     27    1
  2P LOSS WILD-TYPE  309    6
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               27               309
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2P LOSS MUTATED                         0                       30
  2P LOSS WILD-TYPE                       2                      323
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2P LOSS MUTATED                                  1
  2P LOSS WILD-TYPE                                6
D44V9, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      30               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
  2P LOSS MUTATED    26   1   0   4
  2P LOSS WILD-TYPE 292  14   1  17
D44V10, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              26               292
  R1               1                14
  R2               0                 1
  RX               4                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
  2P LOSS MUTATED                                  0    15
  2P LOSS WILD-TYPE                                1   142
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           2    14
  2P LOSS WILD-TYPE                        15   163
D44V11, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15               142
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         14               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"
D44V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  29
  2P LOSS WILD-TYPE  13 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   29
  2P LOSS WILD-TYPE   13  303
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                13
  NOT HISPANIC OR LATINO              29               303
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    25  10
  2Q LOSS WILD-TYPE 204 119
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               35               323 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               119 
$`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        23.38         0.26        13.45 
TCGA-CC-5264 TCGA-CC-A7II TCGA-CC-A7IL TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A39Y 
        3.35        13.12         9.14        83.57        21.76         5.62 
TCGA-DD-A4NJ TCGA-DD-A73B TCGA-DD-AACE TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADN 
       30.51         9.30        63.48        35.67        20.91        29.52 
TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX 
       19.30        20.98         4.64        29.92         9.73         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-FV-A3I1 TCGA-G3-A5SM TCGA-G3-AAV7 TCGA-GJ-A9DB 
        0.20        14.04         8.12        17.10        11.87         2.20 
TCGA-KR-A7K2 TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-WQ-AB4B 
       21.60        15.39         0.76         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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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        17.10        14.76 
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        45.93        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         4.24 
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         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.96        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK 
        7.13        21.34         9.83        12.00        12.56         8.61 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
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-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-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-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-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-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-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       35.05        34.49         0.39        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-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.15        18.61        19.99        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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        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        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       13.91        13.35        12.82        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-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-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10        27.88         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-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        0.89         8.75         2.14        22.92         1.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       31.27        29.79        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        22.95        24.56        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        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        36.10        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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 
        0.99        20.22        24.85        18.28        22.78        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        35.87         0.69        25.15 
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 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 
            13.12             20.22 
[1] "0.2 - 83.6 (13.1)"  "0.0 - 120.8 (20.2)"
[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     155       75         3         53          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               155
  STAGE II                10                75
  STAGE III                0                 3
  STAGE IIIA               7                53
  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   165  82  66  11
D45V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1              17               165
  T2                 10                82
  T3                  8                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"
D45V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    23   0
  2Q LOSS WILD-TYPE 227   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     23    0
  2Q LOSS WILD-TYPE  227    3
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              23               227
  1               0                 3
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    28   0
  2Q LOSS WILD-TYPE 233   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     28    0
  2Q LOSS WILD-TYPE  233    4
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              28               233
  1               0                 4
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    10  26
  2Q LOSS WILD-TYPE 105 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     10   26
  2Q LOSS WILD-TYPE  105  221
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              10               105
  MALE                26               221
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    32   1
  2Q LOSS WILD-TYPE 304   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     32    1
  2Q LOSS WILD-TYPE  304    6
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               32               304
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2Q LOSS MUTATED                         0                       35
  2Q LOSS WILD-TYPE                       2                      318
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2Q LOSS MUTATED                                  1
  2Q LOSS WILD-TYPE                                6
D45V9, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      35               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
  2Q LOSS MUTATED    31   0   0   5
  2Q LOSS WILD-TYPE 287  15   1  16
D45V10, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              31               287
  R1               0                15
  R2               0                 1
  RX               5                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
  2Q LOSS MUTATED                                  0    18
  2Q LOSS WILD-TYPE                                1   139
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           2    16
  2Q LOSS WILD-TYPE                        15   161
D45V11, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         18               139
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         16               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"
D45V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1  32
  2Q LOSS WILD-TYPE  12 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   32
  2Q LOSS WILD-TYPE   12  300
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              32               300
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    33  16
  3P LOSS WILD-TYPE 196 113
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               49               309 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               16               113 
$`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        49.84        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         9.96        10.36 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 
        8.94         7.13        13.12         8.15        79.73       113.00 
TCGA-DD-A1E9 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-AACO 
       90.71        30.61        33.14        26.83        73.81        61.68 
TCGA-DD-AADO TCGA-DD-AADY TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-ED-A66Y TCGA-ED-A7PX 
       14.89        18.25        89.69        72.39         9.73         0.20 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A97K TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25X 
        0.20        13.41         0.20        27.88        51.06        58.49 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC 
       14.70        11.80         2.14        21.60        31.27        13.97 
TCGA-MR-A8JO TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-ZP-A9D1 
       10.85        16.44         1.71         7.04        12.99         0.69 
TCGA-ZS-A9CE 
       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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        22.92         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 
       17.10        14.76         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        23.38 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57        44.42        45.93         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         4.24         2.86         3.19         3.39 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        3.35         3.32         9.86        11.93        11.41         9.99 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
       21.34         9.83        12.00        12.56         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 
        4.60        11.31         9.17         6.94        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33         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-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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78         0.36        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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        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        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
       13.91        13.35        12.82        14.04        13.15        13.35 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        1.84        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-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-A5SM TCGA-G3-A6UC 
       19.23        25.25        22.95        20.42        17.10        22.06 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       12.23        13.55         0.89         8.75        11.87        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD 
       16.83        11.80         2.14        29.79        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        22.95        24.56        20.71         7.53 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        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        36.10         0.76 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       17.59        19.76        15.98        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 
        0.99        20.22        24.85        18.28        22.78        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        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.20              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           113.00            120.82 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            13.97             20.22 
[1] "0.2 - 113.0 (14.0)" "0.0 - 120.8 (20.2)"
[1] "hr=" "1.1"
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     158       70         3         46          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               158
  STAGE II                15                70
  STAGE III                0                 3
  STAGE IIIA              14                46
  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   168  76  57   9
D46V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              14               168
  T2                 16                76
  T3                 17                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"
D46V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    34   1
  3P LOSS WILD-TYPE 216   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     34    1
  3P LOSS WILD-TYPE  216    2
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              34               216
  1               1                 2
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    35   1
  3P LOSS WILD-TYPE 226   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     35    1
  3P LOSS WILD-TYPE  226    3
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              35               226
  1               1                 3
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    19  31
  3P LOSS WILD-TYPE  96 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     19   31
  3P LOSS WILD-TYPE   96  216
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              19                96
  MALE                31               216
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    48   0
  3P LOSS WILD-TYPE 288   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     48    0
  3P LOSS WILD-TYPE  288    7
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               48               288
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3P LOSS MUTATED                         1                       45
  3P LOSS WILD-TYPE                       1                      308
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3P LOSS MUTATED                                  4
  3P LOSS WILD-TYPE                                3
D46V9, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      45               308
  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 271  15   1  18
D46V10, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              47               271
  R1               0                15
  R2               0                 1
  RX               3                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
  3P LOSS MUTATED                                  0    22
  3P LOSS WILD-TYPE                                1   135
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           2    26
  3P LOSS WILD-TYPE                        15   151
D46V11, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         22               135
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         26               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"
D46V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  46
  3P LOSS WILD-TYPE  12 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   46
  3P LOSS WILD-TYPE   12  286
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              46               286
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    27  10
  3Q LOSS WILD-TYPE 202 119
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               37               321 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               119 
$`3Q LOSS MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A112 
       24.89        49.84        18.25        13.02        10.78         5.03 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 
        8.94         7.13        13.12         8.15        79.73       113.00 
TCGA-DD-A1E9 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-AACO TCGA-DD-AADO 
       90.71        33.14        26.83        73.81        61.68        14.89 
TCGA-DD-AADY TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E 
       18.25        89.69        72.39         9.73         0.20        13.41 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 
        1.84         0.20        14.70        11.80         2.14        21.60 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MR-A8JO TCGA-UB-A7MC TCGA-WQ-AB4B TCGA-ZP-A9D1 
       31.27        13.97        10.85        16.44        12.99         0.69 
TCGA-ZS-A9CE 
       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 
       38.40        20.81        22.92         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        17.10        14.76         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        23.38         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       45.93         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         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT 
        2.86         3.19         3.39         4.24         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        9.86         9.96        10.36        11.93        11.41         9.99 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
       21.34         9.83        12.00        12.56         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 
        4.60        11.31         9.17         6.94        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33         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-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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        30.61        32.52        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       30.15        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-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-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-AACP TCGA-DD-AACQ 
        0.30         3.52        58.16        42.81        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-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-AADW TCGA-DD-AAE0 
       66.67        15.58        18.21        18.87        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-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        26.63 
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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        80.71        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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       28.08        13.91        13.35         0.20        12.82        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.15        13.35        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        22.06        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14         1.84        15.78        15.65        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
        2.14        29.79        12.72        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        24.56        20.71         7.53        58.88        26.27 
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        36.10         0.76        17.59        19.76 
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-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 
        0.99        20.22        24.85        18.28        22.78        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        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        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 
            14.70             20.12 
[1] "0.2 - 113.0 (14.7)" "0.0 - 120.8 (20.1)"
[1] "hr=" "1.4"
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     160       74         3         50          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               160
  STAGE II                11                74
  STAGE III                0                 3
  STAGE IIIA              10                50
  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   170  80  62  10
D47V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1              12               170
  T2                 12                80
  T3                 12                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"
D47V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    26   1
  3Q LOSS WILD-TYPE 224   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     26    1
  3Q LOSS WILD-TYPE  224    2
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              26               224
  1               1                 2
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    28   0
  3Q LOSS WILD-TYPE 233   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     28    0
  3Q LOSS WILD-TYPE  233    4
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              28               233
  1               0                 4
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    14  24
  3Q LOSS WILD-TYPE 101 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     14   24
  3Q LOSS WILD-TYPE  101  223
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              14               101
  MALE                24               223
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    37   0
  3Q LOSS WILD-TYPE 299   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     37    0
  3Q LOSS WILD-TYPE  299    7
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               37               299
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3Q LOSS MUTATED                         1                       35
  3Q LOSS WILD-TYPE                       1                      318
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3Q LOSS MUTATED                                  2
  3Q LOSS WILD-TYPE                                5
D47V9, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      35               318
  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 282  15   1  19
D47V10, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              36               282
  R1               0                15
  R2               0                 1
  RX               2                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   140
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           1    20
  3Q LOSS WILD-TYPE                        16   157
D47V11, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17               140
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         20               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"
D47V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  34
  3Q LOSS WILD-TYPE  12 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   34
  3Q LOSS WILD-TYPE   12  298
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              34               298
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    65  38
  4P LOSS WILD-TYPE 164  91
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              103               255 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               38                91 
$`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        49.84        13.02        10.78         0.66 
TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       23.38         5.03        45.93        22.36        17.98        14.60 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A3MC TCGA-CC-A7IE TCGA-CC-A7IF 
       13.45         0.66         3.35        11.93         7.13        21.34 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HV TCGA-CC-A9FS 
       13.12        12.56         8.61         9.14         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EI TCGA-DD-A1EJ 
        8.15        79.73        37.78         7.33         6.02        33.04 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NI TCGA-DD-A4NJ 
       13.64        55.69         5.62        30.61        26.83        30.51 
TCGA-DD-A4NN TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       29.56         0.53        76.41        63.48        12.00        15.42 
TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD8 
       42.81        13.64        51.52        47.67        44.22        40.08 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AAE0 
       13.97        40.47        20.91        66.67        18.87        18.25 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU 
       21.83        18.90        25.08        35.08        89.69        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       80.71        76.18        29.92        13.35        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A496 
       14.04         1.84        19.59         0.62        23.97         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A7M5 TCGA-G3-A7M9 
       81.73        13.68        53.79        58.49        14.70         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-K7-A5RG 
       15.78        11.80         0.89         2.14        22.92        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MI-A75G TCGA-PD-A5DF TCGA-RC-A7SB 
       21.60        31.27        13.97        22.95        21.01        19.33 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       15.52        36.10        19.76        16.44        15.98         7.04 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       12.99        20.22        22.78        13.55        25.15        40.80 
TCGA-ZS-A9CF 
       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 
       38.40        20.81        22.92         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        17.10        14.76         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         4.24         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         9.86         9.96        10.36 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A8HT 
       11.41         9.99         8.94         9.83        12.00         4.60 
TCGA-CC-A8HU TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       11.31        83.57        53.33       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK 
       75.65        11.47        12.95        45.11        49.15        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-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-A4NK 
       33.14        32.52        90.28        30.97        30.15        39.78 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
       35.67       114.35        13.48        11.41        75.65        55.40 
TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.53         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV 
       58.16        61.68        14.20        59.31        51.35        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADF 
       42.58        22.09        40.54        40.83        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-AADS TCGA-DD-AADU TCGA-DD-AADW 
       14.89        15.06        14.33        15.58        18.21        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-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       21.17        23.74        15.72        26.63        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVY 
       50.33        79.07        82.62        59.93        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       62.47        66.25        65.39        49.48        53.69        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E 
       28.08        13.91         9.73         0.20        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
       13.35         0.20        18.74        19.99        20.61         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-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV0 
       17.10        22.06        20.78        11.87        14.14        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       12.23        13.55         8.75        11.87         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
        2.99        37.71        20.75        16.83        11.80         2.14 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       29.79        12.72        12.03         9.57        16.67        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MA 
        3.09        21.04        19.04        15.39         0.76        17.59 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 
        1.71        10.75        10.32        11.34         0.99        24.85 
TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       18.28        35.77        25.71        23.21        35.87         0.69 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       12.99        45.57        11.21 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.20              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            89.69            120.82 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            18.90             19.99 
[1] "0.2 - 89.7 (18.9)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.2"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P LOSS MUTATED        42       31         0         20          3          2
  4P LOSS WILD-TYPE     129       54         3         40          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                 42               129
  STAGE II                31                54
  STAGE III                0                 3
  STAGE IIIA              20                40
  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      44  34  24   4
  4P LOSS WILD-TYPE   138  58  50   8
D48V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              44               138
  T2                 34                58
  T3                 24                50
  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    69   2
  4P LOSS WILD-TYPE 181   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     69    2
  4P LOSS WILD-TYPE  181    1
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              69               181
  1               2                 1
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    78   3
  4P LOSS WILD-TYPE 183   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     78    3
  4P LOSS WILD-TYPE  183    1
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              78               183
  1               3                 1
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    27  79
  4P LOSS WILD-TYPE  88 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     27   79
  4P LOSS WILD-TYPE   88  168
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              27                88
  MALE                79               168
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    98   2
  4P LOSS WILD-TYPE 238   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     98    2
  4P LOSS WILD-TYPE  238    5
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               98               238
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4P LOSS MUTATED                         0                      104
  4P LOSS WILD-TYPE                       2                      249
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4P LOSS MUTATED                                  2
  4P LOSS WILD-TYPE                                5
D48V9, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     104               249
  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    94   3   1   7
  4P LOSS WILD-TYPE 224  12   0  14
D48V10, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              94               224
  R1               3                12
  R2               1                 0
  RX               7                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    54
  4P LOSS WILD-TYPE                                1   103
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           8    43
  4P LOSS WILD-TYPE                         9   134
D48V11, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         54               103
  BLACK OR AFRICAN AMERICAN                      8                 9
  WHITE                                         43               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"
D48V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     7  96
  4P LOSS WILD-TYPE   6 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      7   96
  4P LOSS WILD-TYPE    6  236
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                 6
  NOT HISPANIC OR LATINO              96               236
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    90  53
  4Q LOSS WILD-TYPE 139  76
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              143               215 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               53                76 
$`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        49.84        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        23.38 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        45.93         0.26        22.36        17.98        14.60 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
       13.45         0.66         3.35         9.86        10.36        11.93 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IJ 
        9.99         8.94         7.13        21.34        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        8.61         9.14        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EG 
       79.73        37.78        53.33         7.33         2.60        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       49.15         6.02        33.04        13.64        55.69         5.62 
TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
       30.61        30.15        26.83        30.51        29.56        73.81 
TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF 
        9.30         0.53        76.41        55.40        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS 
       15.42         3.52        58.16        42.81        13.64        59.31 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD8 
       51.52        50.33        46.82         5.62        44.22        40.08 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADO 
       40.83        13.97        40.47        35.67        20.91        14.89 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.06        66.67        18.87        18.25        18.25        18.15 
TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ 
        4.64        21.83        18.90        25.08        35.08        89.69 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAW0 TCGA-ED-A66X 
       59.93        72.39        80.71        76.18        66.25        13.35 
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-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.59         0.62        23.97         8.12         0.33        81.73 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM 
       13.68        58.49        14.86        21.53        25.25        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       14.70         1.84        11.80         0.89         2.14        11.87 
TCGA-GJ-A3OU TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC 
       22.92        17.06        21.60        31.27        12.72        13.97 
TCGA-MI-A75G TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       22.95        19.33        15.39        15.52        36.10         0.76 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       19.76        16.44        15.98         7.04         0.99        12.99 
TCGA-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       20.22        22.78        13.55        25.15        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        38.40 
TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       22.92         8.55         8.61        17.10        14.76         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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A7IG 
        3.39         4.24         3.32         9.96        11.41         9.83 
TCGA-CC-A7IH TCGA-CC-A8HT TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
       12.00         4.60        83.57       113.00         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z 
       11.47        12.95        18.35        21.14        27.19        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        33.14        32.52        90.28 
TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.97        39.78        56.25       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        23.93        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD 
       35.67       114.35        13.48        11.41        75.65        12.53 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACQ 
        6.41        53.19        69.11         0.30        61.68        14.20 
TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       51.35         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       42.58        22.09        40.54        39.52         3.78        37.64 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS 
       35.05        34.49         0.39        29.52        14.33        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 
       18.21        19.30        20.98        18.61        19.99        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        26.63        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW1 
       79.07        82.62        56.48        64.77        62.47        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
        9.73         0.20        13.41         1.84        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       20.61         9.96        11.93        22.85        14.40        60.89 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       19.10        27.88         6.38        12.03         0.03         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CH 
       51.06        53.79        28.27        30.74        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
        5.92        19.53        19.23        22.95        20.42        22.06 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       20.78        11.87        14.14        15.78        15.65        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       13.55         8.75         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QD 
       20.75        16.83        11.80         2.14        29.79        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        24.56        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        17.69        21.01         3.09        21.04 
TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       19.04        17.59         1.71        10.75        10.32        11.34 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        18.28        35.77        25.71        23.21        35.87 
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 
             0.20              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            89.69            120.82 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            17.10             20.78 
[1] "0.2 - 89.7 (17.1)"  "0.0 - 120.8 (20.8)"
[1] "hr=" "1.3"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED        63       39         1         26          4          2
  4Q LOSS WILD-TYPE     108       46         2         34          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                 63               108
  STAGE II                39                46
  STAGE III                1                 2
  STAGE IIIA              26                34
  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      67  41  33   5
  4Q LOSS WILD-TYPE   115  51  41   7
D49V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              67               115
  T2                 41                51
  T3                 33                41
  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   102   2
  4Q LOSS WILD-TYPE 148   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    102    2
  4Q LOSS WILD-TYPE  148    1
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             102               148
  1               2                 1
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   114   3
  4Q LOSS WILD-TYPE 147   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    114    3
  4Q LOSS WILD-TYPE  147    1
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             114               147
  1               3                 1
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    41 105
  4Q LOSS WILD-TYPE  74 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     41  105
  4Q LOSS WILD-TYPE   74  142
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              41                74
  MALE               105               142
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   135   2
  4Q LOSS WILD-TYPE 201   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    135    2
  4Q LOSS WILD-TYPE  201    5
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              135               201
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4Q LOSS MUTATED                         0                      143
  4Q LOSS WILD-TYPE                       2                      210
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4Q LOSS MUTATED                                  3
  4Q LOSS WILD-TYPE                                4
D49V9, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     143               210
  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   133   4   1   8
  4Q LOSS WILD-TYPE 185  11   0  13
D49V10, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             133               185
  R1               4                11
  R2               1                 0
  RX               8                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    80
  4Q LOSS WILD-TYPE                                1    77
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           9    57
  4Q LOSS WILD-TYPE                         8   120
D49V11, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         80                77
  BLACK OR AFRICAN AMERICAN                      9                 8
  WHITE                                         57               120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     7 135
  4Q LOSS WILD-TYPE   6 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      7  135
  4Q LOSS WILD-TYPE    6  197
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                 6
  NOT HISPANIC OR LATINO             135               197
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    16  11
  5P LOSS WILD-TYPE 213 118
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               27               331 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               118 
$`5P LOSS MUTATED`
TCGA-5C-AAPD TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-A3M9 TCGA-CC-A7IE TCGA-CC-A7IJ 
        0.66        46.78         4.24         9.86         7.13        12.56 
TCGA-CC-A7IK TCGA-CC-A8HV TCGA-DD-A11A TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A4NB 
        8.61         9.17         2.60        49.15        33.04        32.52 
TCGA-DD-AACS TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADW 
       59.31        40.83        40.47        37.64        35.67        19.30 
TCGA-DD-AAVQ TCGA-ED-A97K TCGA-ES-A2HS TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A7M9 
       89.69         0.20        22.85         0.33        13.68         1.84 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-WX-AA44 
        2.14        11.87        20.22 

$`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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        38.40        20.81        22.92 
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 
       17.10        14.76         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        23.38 
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        45.93         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-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.35         3.32         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.41         9.99         8.94        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW 
       13.12         9.14         4.60        11.31         6.94         8.15 
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-A1EI 
       19.79        75.65        11.47        12.95        45.11         6.02 
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-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-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-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-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADJ 
       40.08        40.54        13.97        39.52         3.78        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-AAEK TCGA-DD-AAVP 
       26.63        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        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 
       29.92        26.93        28.08        13.91        13.35         9.73 
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-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-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-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       81.73         0.39        51.06        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       22.06        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89         8.75 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83        11.80         2.14        21.60        31.27 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       29.79        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 
       22.95        24.56        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       26.27        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        36.10         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-WX-AA47 
       10.32        11.34         0.99        12.99        24.85        18.28 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        25.15        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.20              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            89.69            120.82 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            13.68             19.79 
[1] "0.2 - 89.7 (13.7)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P LOSS MUTATED        12        5         1          7          1          1
  5P LOSS WILD-TYPE     159       80         2         53          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                 12               159
  STAGE II                 5                80
  STAGE III                1                 2
  STAGE IIIA               7                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
  5P LOSS MUTATED      13   5  10   0
  5P LOSS WILD-TYPE   169  87  64  12
D50V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              13               169
  T2                  5                87
  T3                 10                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"
D50V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    22   1
  5P LOSS WILD-TYPE 228   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     22    1
  5P LOSS WILD-TYPE  228    2
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              22               228
  1               1                 2
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    24   0
  5P LOSS WILD-TYPE 237   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     24    0
  5P LOSS WILD-TYPE  237    4
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              24               237
  1               0                 4
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     7  21
  5P LOSS WILD-TYPE 108 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      7   21
  5P LOSS WILD-TYPE  108  226
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               7               108
  MALE                21               226
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    23   1
  5P LOSS WILD-TYPE 313   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     23    1
  5P LOSS WILD-TYPE  313    6
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               23               313
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5P LOSS MUTATED                         1                       25
  5P LOSS WILD-TYPE                       1                      328
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5P LOSS MUTATED                                  2
  5P LOSS WILD-TYPE                                5
D50V9, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      25               328
  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   2
  5P LOSS WILD-TYPE 293  14   1  19
D50V10, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              25               293
  R1               1                14
  R2               0                 1
  RX               2                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   140
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           1    10
  5P LOSS WILD-TYPE                        16   167
D50V11, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17               140
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         10               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"
D50V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     1  27
  5P LOSS WILD-TYPE  12 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   27
  5P LOSS WILD-TYPE   12  305
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              27               305
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    21  17
  5Q LOSS WILD-TYPE 208 112
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               38               320 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               17               112 
$`5Q LOSS MUTATED`
TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A10S TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A5UD 
        0.66        10.13        46.78         4.24         9.86         9.99 
TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HV TCGA-DD-A11A 
        7.13        13.12        12.56         8.61         9.17         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        20.78         1.84         2.14        11.87        19.76 
TCGA-UB-A7MF TCGA-WX-AA44 
        7.04        20.22 

$`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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        38.40        20.81        22.92 
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 
       17.10        14.76         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        23.38         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        45.93         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         4.24         2.86         3.19         3.39 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.35         3.32         9.96        10.36        11.93        11.41 
TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A8HT 
        8.94        21.34         9.83        12.00         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
       11.31         6.94         8.15        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-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       45.11         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-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        33.14        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-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-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-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-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-AADA TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF 
       44.22        22.09        40.54        13.97        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       37.64        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-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       18.87        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        26.63        23.64        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       35.08        79.07        82.62        59.93        72.39        80.71 
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        29.92        26.93        28.08        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-A7M5 
       25.25        22.95        20.42        17.10        22.06        14.70 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       13.55         0.89         8.75        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        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-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10         0.76        17.59        16.44         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-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       18.28        22.78        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 
       35.87         0.69        25.15        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.20              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            89.69            120.82 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            13.40             19.99 
[1] "0.2 - 89.7 (13.4)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.5"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED        15        7         1         12          1          1
  5Q LOSS WILD-TYPE     156       78         2         48          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                 15               156
  STAGE II                 7                78
  STAGE III                1                 2
  STAGE IIIA              12                48
  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      16   7  16   0
  5Q LOSS WILD-TYPE   166  85  58  12
D51V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              16               166
  T2                  7                85
  T3                 16                58
  T4                  0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    27   1
  5Q LOSS WILD-TYPE 223   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     27    1
  5Q LOSS WILD-TYPE  223    2
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              27               223
  1               1                 2
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    31   0
  5Q LOSS WILD-TYPE 230   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     31    0
  5Q LOSS WILD-TYPE  230    4
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              31               230
  1               0                 4
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    13  26
  5Q LOSS WILD-TYPE 102 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     13   26
  5Q LOSS WILD-TYPE  102  221
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              13               102
  MALE                26               221
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    33   1
  5Q LOSS WILD-TYPE 303   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     33    1
  5Q LOSS WILD-TYPE  303    6
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               33               303
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5Q LOSS MUTATED                         1                       35
  5Q LOSS WILD-TYPE                       1                      318
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5Q LOSS MUTATED                                  3
  5Q LOSS WILD-TYPE                                4
D51V9, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      35               318
  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   2
  5Q LOSS WILD-TYPE 283  13   1  19
D51V10, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              35               283
  R1               2                13
  R2               0                 1
  RX               2                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   136
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           1    17
  5Q LOSS WILD-TYPE                        16   160
D51V11, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         21               136
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         17               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"
D51V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1  38
  5Q LOSS WILD-TYPE  12 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   38
  5Q LOSS WILD-TYPE   12  294
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              38               294
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    15  12
  6P LOSS WILD-TYPE 214 117
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               27               331 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12               117 
$`6P LOSS MUTATED`
TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-A3M9 TCGA-CC-A5UD 
      120.82        56.91        17.98        12.72         9.86         9.99 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE 
      113.00         2.60        21.76        90.71        19.79        11.47 
TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39Z TCGA-DD-A4NH 
       12.95         6.02        33.04        18.35        19.76        30.15 
TCGA-DD-A4NK TCGA-DD-AAEG TCGA-DD-AAVU TCGA-ED-A66Y TCGA-G3-AAV6 TCGA-UB-A7MB 
       39.78        23.64        72.39         9.73         2.14        19.76 
TCGA-UB-A7ME TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       15.98         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        49.84        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        38.40        20.81        22.92         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        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       14.76         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        23.38 
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        45.93         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         4.24         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.35         3.32         9.96        10.36        11.93        11.41 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        8.94         7.13        21.34         9.83        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.56         8.61         9.14         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        7.33         0.46        51.29        79.40        66.31        75.65 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       45.11        49.15        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       32.52        90.28        30.97        26.83        30.51        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-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-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        26.63 
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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        80.71        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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       28.08        13.91        13.35         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-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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       17.10        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        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-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
       36.10         0.76        17.59        16.44         1.71         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       10.75        10.32        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       24.85        18.28        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.69              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           120.82            114.35 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            19.76             19.99 
[1] "0.7 - 120.8 (19.8)" "0.0 - 114.3 (20.0)"
[1] "hr=" "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     161       80         3         52          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               161
  STAGE II                 5                80
  STAGE III                0                 3
  STAGE IIIA               8                52
  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   170  87  65  11
D52V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1              12               170
  T2                  5                87
  T3                  9                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"
D52V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    20   1
  6P LOSS WILD-TYPE 230   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     20    1
  6P LOSS WILD-TYPE  230    2
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              20               230
  1               1                 2
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    21   1
  6P LOSS WILD-TYPE 240   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     21    1
  6P LOSS WILD-TYPE  240    3
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              21               240
  1               1                 3
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    14  13
  6P LOSS WILD-TYPE 101 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     14   13
  6P LOSS WILD-TYPE  101  234
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              14               101
  MALE                13               234
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    23   0
  6P LOSS WILD-TYPE 313   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     23    0
  6P LOSS WILD-TYPE  313    7
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               23               313
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6P LOSS MUTATED                         0                       27
  6P LOSS WILD-TYPE                       2                      326
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6P LOSS MUTATED                                  0
  6P LOSS WILD-TYPE                                7
D52V9, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      27               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
  6P LOSS MUTATED    25   1   0   1
  6P LOSS WILD-TYPE 293  14   1  20
D52V10, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              25               293
  R1               1                14
  R2               0                 1
  RX               1                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   150
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           1    18
  6P LOSS WILD-TYPE                        16   159
D52V11, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7               150
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         18               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"
D52V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  24
  6P LOSS WILD-TYPE  12 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   24
  6P LOSS WILD-TYPE   12  308
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              24               308
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    55  35
  6Q LOSS WILD-TYPE 174  94
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               90               268 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               35                94 
$`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        38.40        20.81         8.61        17.10 
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-CC-A5UD TCGA-CC-A7IL TCGA-CC-A9FS TCGA-DD-A118 
        9.86         9.96         9.99         9.14         6.94       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-A39X TCGA-DD-A39Z TCGA-DD-A3A1 
        6.02        33.04        18.35        55.69        19.76         7.66 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NS 
        0.36        33.14        30.15        30.51        39.78        80.75 
TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACE TCGA-DD-AACH TCGA-DD-AACI 
        1.45        13.48         0.53        63.48         6.41        53.19 
TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADK TCGA-DD-AADL 
       13.64        51.52        42.58        40.08        34.49        20.91 
TCGA-DD-AADP TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE9 TCGA-DD-AAEG 
       15.06        18.87        18.25        20.98        23.74        23.64 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAW3 TCGA-ED-A66Y TCGA-ED-A7PZ 
       59.93        72.39        64.77        53.69         9.73         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A3RK 
       13.41        13.35         1.84         0.20        18.74        11.93 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       22.85        60.89        19.10        27.88         6.38        81.73 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-AAV3 
       51.06        58.49        20.42        22.06        14.70        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5N0 TCGA-MI-A75E TCGA-MI-A75I TCGA-T1-A6J8 
        0.89         2.14        37.71        16.67        20.71         0.76 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-XR-A8TF TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       19.76        15.98        10.75        22.78         0.69        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        49.84        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       11.74        22.92         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        14.76        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        23.38 
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        45.93        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-5264 TCGA-CC-A1HT 
        4.24         3.19         3.39         4.24         3.35         3.32 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       10.36        11.93        11.41         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT 
        9.83        12.00        13.12        12.56         8.61         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
       11.31         9.17         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33         7.33         0.46        51.29        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       75.65        45.11        49.15        13.64        21.14        27.19 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
        5.62        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
      107.11        13.78        30.61        32.52        90.28        30.97 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       26.83        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       35.67       114.35        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.53        12.00        15.42        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-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-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB 
       18.54        21.63        44.22        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-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR 
       35.05         0.39        29.52        14.89        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 
       15.58        18.21        19.30        18.25        18.15        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-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ 
       89.69        82.62        80.71        76.18        56.48        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        49.48        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91        13.35         0.20        12.82        14.04        13.15 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62         9.96        14.40 
TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       23.97         8.12        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-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       22.95        17.10        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-G3-AAV7 
       15.78        15.65        11.80        12.23         8.75        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A5RG 
       22.92         1.02         2.20         2.99        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83        11.80         2.14        21.60        31.27        29.79 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H 
       12.72        13.97        12.03         9.57        22.95        24.56 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        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-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V 
       36.10        17.59        16.44         1.71         7.04        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.20              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           120.82            114.35 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           18.985            20.055 
[1] "0.2 - 120.8 (19.0)" "0.0 - 114.3 (20.1)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED        37       22         0         19          2          4
  6Q LOSS WILD-TYPE     134       63         3         41          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                 37               134
  STAGE II                22                63
  STAGE III                0                 3
  STAGE IIIA              19                41
  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      41  25  21   3
  6Q LOSS WILD-TYPE   141  67  53   9
D53V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1              41               141
  T2                 25                67
  T3                 21                53
  T4                  3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    64   2
  6Q LOSS WILD-TYPE 186   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     64    2
  6Q LOSS WILD-TYPE  186    1
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              64               186
  1               2                 1
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    71   2
  6Q LOSS WILD-TYPE 190   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     71    2
  6Q LOSS WILD-TYPE  190    2
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              71               190
  1               2                 2
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    38  53
  6Q LOSS WILD-TYPE  77 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     38   53
  6Q LOSS WILD-TYPE   77  194
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              38                77
  MALE                53               194
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    84   0
  6Q LOSS WILD-TYPE 252   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     84    0
  6Q LOSS WILD-TYPE  252    7
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               84               252
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6Q LOSS MUTATED                         0                       88
  6Q LOSS WILD-TYPE                       2                      265
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6Q LOSS MUTATED                                  3
  6Q LOSS WILD-TYPE                                4
D53V9, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      88               265
  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    81   4   0   5
  6Q LOSS WILD-TYPE 237  11   1  16
D53V10, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              81               237
  R1               4                11
  R2               0                 1
  RX               5                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
  6Q LOSS MUTATED                                  0    36
  6Q LOSS WILD-TYPE                                1   121
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           3    49
  6Q LOSS WILD-TYPE                        14   128
D53V11, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         36               121
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         49               128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3  83
  6Q LOSS WILD-TYPE  10 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   83
  6Q LOSS WILD-TYPE   10  249
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                10
  NOT HISPANIC OR LATINO              83               249
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     7   9
  7P LOSS WILD-TYPE 222 120
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               16               342 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                9               120 
$`7P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A5UD TCGA-CC-A7IG 
       45.93        22.36         3.19         9.86         9.99         9.83 
TCGA-DD-A1EF TCGA-DD-A39X TCGA-DD-AACB TCGA-DD-AADB TCGA-DD-AADN TCGA-EP-A2KB 
       12.95        55.69        76.41        40.83        29.52        19.59 
TCGA-FV-A3I1 TCGA-K7-A5RG TCGA-RC-A7SK TCGA-WX-AA44 
        8.12        17.06        15.52        20.22 

$`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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        38.40        20.81        22.92 
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        17.10        14.76         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        23.38         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         4.24         2.86         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.35         3.32         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II 
       11.41         8.94         7.13        21.34        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.56         8.61         9.14         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        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-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-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-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-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-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-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-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-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        26.63        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-AAVV 
       79.07        89.69        82.62        59.93        72.39        80.71 
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        29.92        26.93        28.08        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-A12J 
       13.15        13.41        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-A2HS 
       19.99        20.61         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-A3R2 
       14.40        60.89        23.97        19.10        27.88         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-A6UC TCGA-G3-A7M5 
       25.25        22.95        20.42        17.10        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        22.92         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        16.83        11.80         2.14        21.60        31.27 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       29.79        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 
       22.95        24.56        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       26.27        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        36.10         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-WX-AA47 TCGA-XR-A8TF 
       11.34         0.99        12.99        24.85        18.28        22.78 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        79.30        11.21 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             3.19              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            76.41            120.82 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           18.325            19.775 
[1] "3.2 - 76.4 (18.3)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.8"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P LOSS MUTATED         9        5         0          2          0          0
  7P LOSS WILD-TYPE     162       80         3         58          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                  9               162
  STAGE II                 5                80
  STAGE III                0                 3
  STAGE IIIA               2                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
  7P LOSS MUTATED       9   5   2   0
  7P LOSS WILD-TYPE   173  87  72  12
D54V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               9               173
  T2                  5                87
  T3                  2                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"
D54V5, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    10   0
  7P LOSS WILD-TYPE 240   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     10    0
  7P LOSS WILD-TYPE  240    3
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              10               240
  1               0                 3
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    11   0
  7P LOSS WILD-TYPE 250   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     11    0
  7P LOSS WILD-TYPE  250    4
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              11               250
  1               0                 4
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     8   8
  7P LOSS WILD-TYPE 107 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      8    8
  7P LOSS WILD-TYPE  107  239
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               8               107
  MALE                 8               239
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    14   1
  7P LOSS WILD-TYPE 322   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     14    1
  7P LOSS WILD-TYPE  322    6
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               14               322
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7P LOSS MUTATED                         0                       16
  7P LOSS WILD-TYPE                       2                      337
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7P LOSS MUTATED                                  0
  7P LOSS WILD-TYPE                                7
D54V9, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      16               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
  7P LOSS MUTATED    14   0   0   2
  7P LOSS WILD-TYPE 304  15   1  19
D54V10, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              14               304
  R1               0                15
  R2               0                 1
  RX               2                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   149
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           1     7
  7P LOSS WILD-TYPE                        16   170
D54V11, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8               149
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                          7               170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  14
  7P LOSS WILD-TYPE  12 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   14
  7P LOSS WILD-TYPE   12  318
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              14               318
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     7  14
  7Q LOSS WILD-TYPE 222 115
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               21               337 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               14               115 
$`7Q LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-CC-A5UC TCGA-CC-A5UD 
       48.99        45.93        22.36         3.19        11.41         9.99 
TCGA-CC-A7IG TCGA-DD-A1EF TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-AACB TCGA-DD-AACZ 
        9.83        12.95        13.64        55.69        76.41         5.62 
TCGA-DD-AADB TCGA-DD-AADF TCGA-ED-A7PX TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-G3-A25S 
       40.83         3.78         0.20         1.84        19.59        13.68 
TCGA-K7-A5RG TCGA-QA-A7B7 TCGA-WX-AA44 
       17.06         3.09        20.22 

$`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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        38.40        20.81        22.92 
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        17.10        14.76         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 
       23.38         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         4.24         2.86         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.35         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        8.94         7.13        21.34        12.00        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        8.61         9.14         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        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-A1EG 
       79.40        66.31        19.79        75.65        11.47        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       49.15         6.02        33.04        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-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-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-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-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-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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       26.93        28.08        13.91        13.35         9.73        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-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-A496 TCGA-FV-A4ZP 
        8.12         6.38        12.03         0.03         0.33        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        25.25        22.95        20.42        17.10        22.06 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       14.70        20.78        11.87        14.14         1.84        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        16.83        11.80         2.14        21.60 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       31.27        29.79        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        22.95        24.56        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        26.27        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        36.10         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-WX-AA47 
       10.32        11.34         0.99        12.99        24.85        18.28 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        25.15        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       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 
            13.64             19.99 
[1] "0.2 - 76.4 (13.6)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "2.6"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q LOSS MUTATED        10        7         0          4          0          0
  7Q LOSS WILD-TYPE     161       78         3         56          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                 10               161
  STAGE II                 7                78
  STAGE III                0                 3
  STAGE IIIA               4                56
  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      10   7   4   0
  7Q LOSS WILD-TYPE   172  85  70  12
D55V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1              10               172
  T2                  7                85
  T3                  4                70
  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 236   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     14    0
  7Q LOSS WILD-TYPE  236    3
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              14               236
  1               0                 3
[1] 2 2
[1] FALSE
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    17   0
  7Q LOSS WILD-TYPE 244   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     17    0
  7Q LOSS WILD-TYPE  244    4
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              17               244
  1               0                 4
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    12   9
  7Q LOSS WILD-TYPE 103 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     12    9
  7Q LOSS WILD-TYPE  103  238
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              12               103
  MALE                 9               238
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    19   1
  7Q LOSS WILD-TYPE 317   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     19    1
  7Q LOSS WILD-TYPE  317    6
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               19               317
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7Q LOSS MUTATED                         0                       21
  7Q LOSS WILD-TYPE                       2                      332
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7Q LOSS MUTATED                                  0
  7Q LOSS WILD-TYPE                                7
D55V9, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      21               332
  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   3
  7Q LOSS WILD-TYPE 302  13   1  18
D55V10, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              16               302
  R1               2                13
  R2               0                 1
  RX               3                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
  7Q LOSS MUTATED                                  0    10
  7Q LOSS WILD-TYPE                                1   147
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           3     8
  7Q LOSS WILD-TYPE                        14   169
D55V11, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10               147
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                          8               169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  19
  7Q LOSS WILD-TYPE  12 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   19
  7Q LOSS WILD-TYPE   12  313
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              19               313
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   121  63
  8P LOSS WILD-TYPE 108  66
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              184               174 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               63                66 
$`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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        11.74        38.40         1.18         8.55        13.02 
TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       17.10         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        45.93         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A7IE 
       12.72        13.45         0.66         3.19         3.39         7.13 
TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
        9.83        13.12        12.56         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        9.17         6.94         8.15        79.73        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL 
      113.00        21.76        11.47        45.11        33.04        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 
       21.14        55.69         5.62        19.76        25.81        17.59 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NH 
       13.78         0.36        30.61        33.14        90.28        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A 
       26.83        30.51        39.78         0.30        78.84        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-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACM 
       76.41        55.40        63.48        15.42         6.41        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
       42.81        61.68        13.64        14.20        59.31        51.52 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       47.67         4.50        42.58        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN 
       13.97        37.64        35.67        34.49         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADV TCGA-DD-AAE0 TCGA-DD-AAE4 
       14.89        15.06        14.33        18.87        18.25        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-AAEE TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       26.63        25.78        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW3 TCGA-ED-A7PY 
       72.39        64.77        62.47        66.25        53.69        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20        14.04         1.84        18.74        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        22.85        14.40        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25S 
       27.88         8.12         6.38         0.03        81.73        13.68 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A6UC TCGA-G3-A7M5 
       28.27        30.74        22.13        19.53        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 
       20.78         1.84        15.65        12.23         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-LG-A9QC TCGA-MI-A75C 
        2.14        11.87         2.99        16.83        13.97         9.57 
TCGA-MI-A75E TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       16.67        20.71        26.27        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       21.04        19.04        15.39        15.52        36.10         0.76 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76         1.71        15.98         7.04        10.75        11.34 
TCGA-WX-AA47 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       18.28        13.55        35.77        23.21        35.87        25.15 
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        22.92         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        14.76        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        23.38         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-5264 
       44.81        36.66         4.24         2.86         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IK TCGA-DD-A114 
        9.99         8.94        21.34        12.00         8.61        37.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       18.35        27.19         7.66        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
      107.11        32.52        30.97        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
      108.76        12.26        80.75        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       75.65        12.53        12.00        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
        3.52        51.35        50.33        46.82         5.59         5.62 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADE 
       18.54        21.63        44.22        22.09        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        3.78        35.05        20.91        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAEA 
       19.30        18.25        18.15        20.98        18.61        18.90 
TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       23.64        50.33        35.08        80.71        76.18        56.48 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        49.48        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       13.35         9.73         0.20        13.15        13.41        13.35 
TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A496 
        0.20        19.59         9.96        60.89        12.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39        51.06        53.79        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
       25.64         5.92        19.23        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 
       17.10        11.87        14.14        15.78        11.80        13.55 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
       22.92         1.02         2.20        37.71        20.75        17.06 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       11.80         2.14        21.60        31.27        29.79        12.72 
TCGA-LG-A9QD TCGA-MI-A75G TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       12.03        22.95        24.56         7.53        10.85        58.88 
TCGA-RC-A7SB TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       19.33        17.59        16.44        10.32         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-XR-A8TF TCGA-ZP-A9CY TCGA-ZP-A9D1 TCGA-ZS-A9CD 
       20.22        24.85        22.78        25.71         0.69        45.57 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.03              0.20 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           114.35            120.82 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            19.76             19.69 
[1] "0.0 - 114.3 (19.8)" "0.2 - 120.8 (19.7)"
[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         27          7          4
  8P LOSS WILD-TYPE      84       40         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                84
  STAGE II                45                40
  STAGE III                0                 3
  STAGE IIIA              27                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 35  5
  8P LOSS WILD-TYPE    88 40 39  7
D56V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              94                88
  T2                 52                40
  T3                 35                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 129   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    121    3
  8P LOSS WILD-TYPE  129    0
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             121               129
  1               3                 0
[1] 2 2
[1] FALSE
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   130   2
  8P LOSS WILD-TYPE 131   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    130    2
  8P LOSS WILD-TYPE  131    2
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             130               131
  1               2                 2
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    60 126
  8P LOSS WILD-TYPE  55 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     60  126
  8P LOSS WILD-TYPE   55  121
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              60                55
  MALE               126               121
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   173   4
  8P LOSS WILD-TYPE 163   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    173    4
  8P LOSS WILD-TYPE  163    3
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              173               163
  YES               4                 3
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8P LOSS MUTATED                         0                      185
  8P LOSS WILD-TYPE                       2                      168
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8P LOSS MUTATED                                  1
  8P LOSS WILD-TYPE                                6
D56V9, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     185               168
  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   164   9   0   9
  8P LOSS WILD-TYPE 154   6   1  12
D56V10, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             164               154
  R1               9                 6
  R2               0                 1
  RX               9                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1    76
  8P LOSS WILD-TYPE                                0    81
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          13    91
  8P LOSS WILD-TYPE                         4    86
D56V11, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         76                81
  BLACK OR AFRICAN AMERICAN                     13                 4
  WHITE                                         91                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     7 171
  8P LOSS WILD-TYPE   6 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      7  171
  8P LOSS WILD-TYPE    6  161
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                 6
  NOT HISPANIC OR LATINO             171               161
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    26  15
  8Q LOSS WILD-TYPE 203 114
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               41               317 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               114 
$`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        45.93        22.36 
TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A7IE TCGA-CC-A8HU TCGA-DD-A115 TCGA-DD-A3A0 
        0.66         3.19         7.13        11.31        83.57        25.81 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NK TCGA-DD-A73C TCGA-DD-AACE TCGA-DD-AACY 
       30.61        33.14        39.78        23.05        63.48        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD8 TCGA-DD-AADP TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE6 
        4.50        40.08        15.06        18.87        19.30         4.64 
TCGA-DD-AAEB TCGA-DD-AAVU TCGA-ED-A7PY TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25V 
       15.72        72.39        12.82        27.88         0.03        28.27 
TCGA-G3-A7M9 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-NI-A8LF TCGA-QA-A7B7 
        1.84        12.23         0.89         2.14        26.27         3.09 
TCGA-RC-A7S9 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-WJ-A86L TCGA-ZS-A9CF 
       21.04         0.76         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        49.84        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        38.40        20.81        22.92         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        17.10 
TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       14.76        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        23.38         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         4.24         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.39         4.24         3.35         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF 
       10.36        11.93        11.41         9.99         8.94        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
        4.60         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-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-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
      107.11        13.78         0.36        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-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
        9.30        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-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62        18.54        21.63        42.58        44.22        22.09 
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-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       29.52        14.89        14.33        66.67        15.58        18.21 
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-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEE 
       21.17        21.83        23.74        18.90        25.08        26.63 
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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        80.71        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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
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-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.10         8.12         6.38        12.03         0.33        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25X 
        0.39        13.68        51.06        53.79        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        25.25        22.95        20.42        17.10        22.06 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       11.80        13.55         8.75        11.87        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       11.80         2.14        21.60        31.27        29.79        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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       20.71         7.53        10.85        58.88        17.69        21.01 
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        36.10        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-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
        0.99        12.99        20.22        24.85        18.28        22.78 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        11.21 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.03              0.20 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            83.57            120.82 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            19.30             19.76 
[1] "0.0 - 83.6 (19.3)"  "0.2 - 120.8 (19.8)"
[1] "hr=" "1.2"
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     154       75         3         51          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               154
  STAGE II                10                75
  STAGE III                0                 3
  STAGE IIIA               9                51
  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   164  80  64  10
D57V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1              18               164
  T2                 12                80
  T3                 10                64
  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 225   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     25    1
  8Q LOSS WILD-TYPE  225    2
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              25               225
  1               1                 2
[1] 2 2
[1] FALSE
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    31   1
  8Q LOSS WILD-TYPE 230   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     31    1
  8Q LOSS WILD-TYPE  230    3
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              31               230
  1               1                 3
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    19  23
  8Q LOSS WILD-TYPE  96 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     19   23
  8Q LOSS WILD-TYPE   96  224
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              19                96
  MALE                23               224
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    38   0
  8Q LOSS WILD-TYPE 298   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     38    0
  8Q LOSS WILD-TYPE  298    7
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               38               298
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8Q LOSS MUTATED                         0                       41
  8Q LOSS WILD-TYPE                       2                      312
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8Q LOSS MUTATED                                  1
  8Q LOSS WILD-TYPE                                6
D57V9, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      41               312
  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 282  13   1  17
D57V10, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              36               282
  R1               2                13
  R2               0                 1
  RX               4                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
  8Q LOSS MUTATED                                  0    16
  8Q LOSS WILD-TYPE                                1   141
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           2    24
  8Q LOSS WILD-TYPE                        15   153
D57V11, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         16               141
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         24               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"
D57V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  39
  8Q LOSS WILD-TYPE  12 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   39
  8Q LOSS WILD-TYPE   12  293
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              39               293
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    67  46
  9P LOSS WILD-TYPE 162  83
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              113               245 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               46                83 
$`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        49.84        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        45.93 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
       17.98        14.60         4.24         4.24         3.32         9.86 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG 
       10.36        11.93         9.99         8.94        21.34         9.83 
TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
       12.56         9.14        11.31         6.94         8.15        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33         7.33         2.60         0.46        21.76 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X 
       12.95        45.11         6.02        33.04        18.35        55.69 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NO 
        5.62        25.81        30.61        90.28        26.83        73.81 
TCGA-DD-AA3A TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACU 
       13.48        63.48        15.42        61.68        13.64        51.52 
TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AADC TCGA-DD-AADK TCGA-DD-AADL 
       46.82         5.62        42.58        13.97        34.49        20.91 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADV TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 
       14.89        15.06        18.87        18.15        18.61         4.64 
TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU 
       21.83        25.08        26.63        35.08        89.69        72.39 
TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PZ 
       76.18        62.47        66.25        29.92        13.35         0.20 
TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A3I1 
       13.15         0.20         0.62        11.93        23.97         8.12 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-G3-AAV7 
       13.68        51.06        14.70        11.80         2.14        11.87 
TCGA-GJ-A9DB TCGA-KR-A7K8 TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7SB 
        2.20        29.79        22.95        20.71        26.27        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7ME 
       19.04        15.39        15.52        36.10         0.76        15.98 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       10.75         0.99        12.99        35.87        25.15 

$`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        38.40        22.92         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        17.10        14.76         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        23.38         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-5264 TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7II 
        3.35         9.96        11.41         7.13        12.00        13.12 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A11D 
        8.61         4.60         9.17        37.78       113.00        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A1 
       49.15        13.64        21.14        27.19        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
        0.36        33.14        32.52        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-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       76.41        55.40        12.53        12.00         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-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       59.31        51.35        50.33         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        21.63        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.83        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       35.05         0.39        29.52        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 
       18.21        19.30        18.25        18.25        20.98        19.99 
TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEG TCGA-DD-AAEH 
       21.17        23.74        18.90        15.72        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVX 
       50.33        79.07        82.62        59.93        80.71        56.48 
TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       64.77        65.39        49.48        53.69        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E 
       13.91         9.73         0.20        12.82        14.04        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-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        9.96        22.85        14.40        60.89        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-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        22.06        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14         1.84        15.78        15.65        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 
        0.89         8.75        22.92         1.02         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83        11.80         2.14        21.60 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       31.27        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 
       24.56         7.53        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-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
        7.04        10.32        11.34        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D1 
       22.78        13.55        35.77        25.71        23.21         0.69 
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 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.20              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            90.28            120.82 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            18.15             20.42 
[1] "0.2 - 90.3 (18.1)"  "0.0 - 120.8 (20.4)"
[1] "hr=" "1.3"
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     122       58         3         40          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               122
  STAGE II                27                58
  STAGE III                0                 3
  STAGE IIIA              20                40
  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   128  61  48   8
D58V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              54               128
  T2                 31                61
  T3                 26                48
  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 170   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     80    2
  9P LOSS WILD-TYPE  170    1
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              80               170
  1               2                 1
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    84   3
  9P LOSS WILD-TYPE 177   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     84    3
  9P LOSS WILD-TYPE  177    1
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              84               177
  1               3                 1
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    29  86
  9P LOSS WILD-TYPE  86 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     29   86
  9P LOSS WILD-TYPE   86  161
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              29                86
  MALE                86               161
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   105   2
  9P LOSS WILD-TYPE 231   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    105    2
  9P LOSS WILD-TYPE  231    5
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              105               231
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9P LOSS MUTATED                         0                      113
  9P LOSS WILD-TYPE                       2                      240
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9P LOSS MUTATED                                  2
  9P LOSS WILD-TYPE                                5
D58V9, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     113               240
  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 219   9   0  14
D58V10, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              99               219
  R1               6                 9
  R2               1                 0
  RX               7                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
  9P LOSS MUTATED                                  0    59
  9P LOSS WILD-TYPE                                1    98
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           6    49
  9P LOSS WILD-TYPE                        11   128
D58V11, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         59                98
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         49               128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2 110
  9P LOSS WILD-TYPE  11 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2  110
  9P LOSS WILD-TYPE   11  222
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO             110               222
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    62  42
  9Q LOSS WILD-TYPE 167  87
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              104               254 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               42                87 
$`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        49.84        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        45.93        17.98 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
       14.60         4.24         2.86         4.24         3.32         9.86 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IJ TCGA-CC-A7IL 
       10.36        11.93         8.94        21.34        12.56         9.14 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
        8.15        79.73        53.33         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       21.76        12.95        45.11         6.02        33.04        18.35 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NO 
       55.69         5.62        30.61        33.14        26.83        73.81 
TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACU 
       13.48        76.41        63.48        61.68        13.64        51.52 
TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADO 
        5.62        42.58        40.08        34.49        20.91        14.89 
TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ 
       18.87        21.83        18.90        25.08        35.08        89.69 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X 
       72.39        76.18        62.47        66.25        29.92        13.35 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A3I0 
        0.20        13.15         0.62        11.93        23.97        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CH 
        8.12         6.38        12.03        13.68        51.06        25.64 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-MI-A75G 
       14.70        11.80         2.14        11.87         2.20        22.95 
TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       20.71        26.27        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 
       36.10         0.76        15.98         7.04        10.75        12.99 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       35.87        25.15 

$`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        38.40        22.92         8.55 
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.61         0.66        17.10        14.76         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        23.38         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-5264 TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IG 
        3.35         9.96        11.41         9.99         7.13         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.00        13.12         8.61         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 
        6.94        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        26.63        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY 
       79.07        82.62        59.93        80.71        56.48        64.77 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        49.48        53.69        26.93        28.08        13.91 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 
        9.73         0.20        12.82        14.04        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-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A495 
        9.96        22.85        14.40        60.89        19.10         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-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        22.13         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        22.06 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       12.23        13.55         0.89         8.75        22.92         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        24.56         7.53        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-UB-A7MA 
       58.88        17.69        21.01         3.09        21.04        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       19.76        16.44         1.71        10.32        11.34         0.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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 
             0.20              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            89.69            120.82 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            18.30             20.17 
[1] "0.2 - 89.7 (18.3)"  "0.0 - 120.8 (20.2)"
[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     127       60         3         44          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               127
  STAGE II                25                60
  STAGE III                0                 3
  STAGE IIIA              16                44
  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   133  62  53   7
D59V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1              49               133
  T2                 30                62
  T3                 21                53
  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 183   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     67    3
  9Q LOSS WILD-TYPE  183    0
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              67               183
  1               3                 0
[1] 2 2
[1] FALSE
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    71   3
  9Q LOSS WILD-TYPE 190   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     71    3
  9Q LOSS WILD-TYPE  190    1
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              71               190
  1               3                 1
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    28  77
  9Q LOSS WILD-TYPE  87 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     28   77
  9Q LOSS WILD-TYPE   87  170
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              28                87
  MALE                77               170
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    96   2
  9Q LOSS WILD-TYPE 240   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     96    2
  9Q LOSS WILD-TYPE  240    5
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               96               240
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9Q LOSS MUTATED                         0                      103
  9Q LOSS WILD-TYPE                       2                      250
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9Q LOSS MUTATED                                  2
  9Q LOSS WILD-TYPE                                5
D59V9, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     103               250
  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 229  10   0  13
D59V10, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              89               229
  R1               5                10
  R2               1                 0
  RX               8                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0    50
  9Q LOSS WILD-TYPE                                1   107
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           6    49
  9Q LOSS WILD-TYPE                        11   128
D59V11, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         50               107
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         49               128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2 102
  9Q LOSS WILD-TYPE  11 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2  102
  9Q LOSS WILD-TYPE   11  230
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO             102               230
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    32  11
  10P LOSS WILD-TYPE 197 118
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                43                315 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                11                118 
$`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        45.93        17.98        18.48        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A7II 
       13.45         0.66         9.86         9.96        11.93        13.12 
TCGA-DD-A11C TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NQ TCGA-DD-AACG TCGA-DD-AACO 
       21.76         5.62        26.83        12.26        15.42        61.68 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADR TCGA-DD-AAVU 
       51.52        50.33        40.08        40.54        66.67        72.39 
TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A25X 
        0.20        14.04         0.20        23.97        27.88        58.49 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 
       14.70        11.80         0.89        17.06        21.60        31.27 
TCGA-NI-A4U2 TCGA-QA-A7B7 TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       58.88         3.09        36.10         0.99         0.69        40.80 
TCGA-ZS-A9CF 
       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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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 
       17.10        14.76         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 
       23.38         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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A5UC 
        3.39         4.24         3.35         3.32        10.36        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.56         8.61         9.14         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        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-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-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
      108.76         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-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       63.48        12.00         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-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       51.35        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-AADB 
       18.54        21.63        42.58        44.22        22.09        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-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       15.06        14.33        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        26.63        23.64        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        80.71        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        29.92        26.93        28.08        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-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        1.84        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-A2QR 
        9.96        11.93        22.85        14.40        60.89        19.10 
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-A25W 
        0.39        13.68        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-A5SM TCGA-G3-A6UC 
       19.23        25.25        22.95        20.42        17.10        22.06 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       12.23        13.55         8.75         2.14        11.87        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        20.75        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       11.80         2.14        29.79        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        22.95        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SB 
       10.85        26.27        17.69        21.01        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        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-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
       11.34        12.99        20.22        24.85        18.28        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       12.99        45.57        11.21 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.20               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             79.30             120.82 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             18.48              19.76 
[1] "0.2 - 79.3 (18.5)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
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     156       72         3         51          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                156
  STAGE II                 13                 72
  STAGE III                 0                  3
  STAGE IIIA                9                 51
  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   165  78  63  10
D60V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1               17                165
  T2                  14                 78
  T3                  11                 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"
D60V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    25   1
  10P LOSS WILD-TYPE 225   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     25    1
  10P LOSS WILD-TYPE  225    2
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               25                225
  1                1                  2
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    31   0
  10P LOSS WILD-TYPE 230   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     31    0
  10P LOSS WILD-TYPE  230    4
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               31                230
  1                0                  4
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    13  31
  10P LOSS WILD-TYPE 102 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     13   31
  10P LOSS WILD-TYPE  102  216
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               13                102
  MALE                 31                216
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    43   0
  10P LOSS WILD-TYPE 293   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     43    0
  10P LOSS WILD-TYPE  293    7
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                43                293
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10P LOSS MUTATED                         0                       41
  10P LOSS WILD-TYPE                       2                      312
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10P LOSS MUTATED                                  3
  10P LOSS WILD-TYPE                                4
D60V9, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       41                312
  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 279  14   1  17
D60V10, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               39                279
  R1                1                 14
  R2                0                  1
  RX                4                 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
  10P LOSS MUTATED                                  0    19
  10P LOSS WILD-TYPE                                1   138
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           5    20
  10P LOSS WILD-TYPE                        12   157
D60V11, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          19                138
  BLACK OR AFRICAN AMERICAN                       5                 12
  WHITE                                          20                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"
D60V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  39
  10P LOSS WILD-TYPE  12 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   39
  10P LOSS WILD-TYPE   12  293
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               39                293
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    45  28
  10Q LOSS WILD-TYPE 184 101
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                73                285 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                28                101 
$`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        45.93        17.98        18.48        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
       13.45         0.66         2.86         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A8HT 
        9.96        11.93         9.99         8.94        13.12         4.60 
TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y 
       37.78         2.60        21.76        45.11        13.64         5.62 
TCGA-DD-A4NI TCGA-DD-A4NQ TCGA-DD-AACG TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACU 
       26.83        12.26        15.42        61.68        14.20        51.52 
TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA 
       50.33         5.62        42.58        44.22        40.08        40.54 
TCGA-DD-AADL TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE8 TCGA-ED-A459 TCGA-ED-A7PX 
       20.91        66.67        18.25        21.83        29.92         0.20 
TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A496 
       14.04         1.84         0.20        23.97        27.88         0.33 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A5SJ TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV4 
       53.79        58.49        22.95        14.70        11.80         0.89 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-QA-A7B7 
       17.06        21.60        31.27        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        36.10         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        49.84        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       38.40        20.81        22.92         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        17.10        14.76         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 
       23.38         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         4.24         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
        4.24        10.36        11.41         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV 
       12.00        12.56         8.61         9.14        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        6.94         8.15        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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        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        26.93        28.08        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-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.35        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-A2QR 
        9.96        11.93        22.85        14.40        60.89        19.10 
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-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        22.06        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 
        1.84        15.78        15.65        12.23        13.55         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 
       37.71        20.75        16.83        11.80         2.14        29.79 
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        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       24.56        20.71         7.53        26.27        17.69        21.01 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       21.04        19.04        15.39         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       16.44        15.98         7.04        10.75        10.32        11.34 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 
       12.99        20.22        24.85        18.28        22.78        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        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.20               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             66.67             120.82 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             15.52              20.22 
[1] "0.2 - 66.7 (15.5)"  "0.0 - 120.8 (20.2)"
[1] "hr=" "1.4"
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     141       68         3         46          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                141
  STAGE II                 17                 68
  STAGE III                 0                  3
  STAGE IIIA               14                 46
  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   150  72  57   7
D61V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1               32                150
  T2                  20                 72
  T3                  17                 57
  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 201   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     49    1
  10Q LOSS WILD-TYPE  201    2
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               49                201
  1                1                  2
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    55   0
  10Q LOSS WILD-TYPE 206   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     55    0
  10Q LOSS WILD-TYPE  206    4
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               55                206
  1                0                  4
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    21  53
  10Q LOSS WILD-TYPE  94 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     21   53
  10Q LOSS WILD-TYPE   94  194
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               21                 94
  MALE                 53                194
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    70   1
  10Q LOSS WILD-TYPE 266   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     70    1
  10Q LOSS WILD-TYPE  266    6
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                70                266
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10Q LOSS MUTATED                         1                       69
  10Q LOSS WILD-TYPE                       1                      284
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10Q LOSS MUTATED                                  4
  10Q LOSS WILD-TYPE                                3
D61V9, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       69                284
  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 255  12   1  14
D61V10, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               63                255
  R1                3                 12
  R2                0                  1
  RX                7                 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
  10Q LOSS MUTATED                                  0    38
  10Q LOSS WILD-TYPE                                1   119
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          10    26
  10Q LOSS WILD-TYPE                         7   151
D61V11, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          38                119
  BLACK OR AFRICAN AMERICAN                      10                  7
  WHITE                                          26                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"
D61V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     2  67
  10Q LOSS WILD-TYPE  11 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   67
  10Q LOSS WILD-TYPE   11  265
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               67                265
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    35  24
  11P LOSS WILD-TYPE 194 105
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                59                299 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                105 
$`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        49.84        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        14.76        37.32        46.78         5.03        45.93 
TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A7IJ TCGA-CC-A7IK 
        3.35         9.86         9.96        11.93        12.56         8.61 
TCGA-CC-A7IL TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EJ 
        9.14        79.73        83.57        90.71        12.95        33.04 
TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AACB TCGA-DD-AACO 
       55.69        32.52        90.28        26.83        76.41        61.68 
TCGA-DD-AACP TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADN TCGA-DD-AADO 
       13.64        44.22        22.09        40.47        29.52        14.89 
TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC 
       18.61        35.08         0.20        14.04         1.84         0.62 
TCGA-FV-A2QQ TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ TCGA-G3-A7M9 
       23.97         0.33        81.73        13.68        22.95         1.84 
TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G 
       11.80         2.14        11.87        21.60        31.27        22.95 
TCGA-RC-A7SB TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-YA-A8S7 
       19.33        36.10        17.59        16.44        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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        22.92         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 
       17.10         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        23.38         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         4.24 
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        10.36 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       12.00        13.12         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        8.15        37.78        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65        11.47        45.11        49.15         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        27.19         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-A4NF TCGA-DD-A4NH 
       13.78         0.36        30.61        33.14        30.97        30.15 
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-AACQ TCGA-DD-AACS TCGA-DD-AACT 
        3.52        58.16        42.81        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-AAD8 TCGA-DD-AADA 
        4.50        18.54        21.63        42.58        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-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ 
       35.05        34.49        20.91         0.39        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-AAEE 
       21.83        23.74        18.90        15.72        25.08        26.63 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       23.64        25.78        50.33        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
       12.82        13.15        13.41        13.35         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        20.61        19.59         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        60.89        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       12.03         0.03         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM 
        5.92        19.53        19.23        25.25        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       22.06        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A3OU 
       15.65        12.23        13.55         0.89         8.75        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       16.83        11.80         2.14        29.79        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        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MB 
       21.04        19.04        15.39        15.52         0.76        19.76 
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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
        0.99        12.99        20.22        24.85        18.28        22.78 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        35.87         0.69        25.15 
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 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.20               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             90.71             120.82 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             18.61              19.79 
[1] "0.2 - 90.7 (18.6)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
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     152       69         3         44          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                152
  STAGE II                 16                 69
  STAGE III                 0                  3
  STAGE IIIA               16                 44
  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   161  73  54  11
D62V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               21                161
  T2                  19                 73
  T3                  20                 54
  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 209   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     41    2
  11P LOSS WILD-TYPE  209    1
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               41                209
  1                2                  1
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    46   1
  11P LOSS WILD-TYPE 215   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     46    1
  11P LOSS WILD-TYPE  215    3
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               46                215
  1                1                  3
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    18  43
  11P LOSS WILD-TYPE  97 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     18   43
  11P LOSS WILD-TYPE   97  204
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               18                 97
  MALE                 43                204
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    57   1
  11P LOSS WILD-TYPE 279   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     57    1
  11P LOSS WILD-TYPE  279    6
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                57                279
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11P LOSS MUTATED                         1                       57
  11P LOSS WILD-TYPE                       1                      296
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11P LOSS MUTATED                                  3
  11P LOSS WILD-TYPE                                4
D62V9, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       57                296
  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 264  11   1  18
D62V10, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               54                264
  R1                4                 11
  R2                0                  1
  RX                3                 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 LOSS MUTATED                                  0    25
  11P LOSS WILD-TYPE                                1   132
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           3    33
  11P LOSS WILD-TYPE                        14   144
D62V11, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          25                132
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          33                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"
D62V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4  53
  11P LOSS WILD-TYPE   9 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4   53
  11P LOSS WILD-TYPE    9  279
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  9
  NOT HISPANIC OR LATINO               53                279
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    42  26
  11Q LOSS WILD-TYPE 187 103
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                68                290 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                26                103 
$`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        49.84        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        14.76        27.91        37.32        46.78         5.03 
TCGA-BC-A217 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-CC-A5UD 
       45.93         4.24         3.35         9.86        11.93         9.99 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A 
       12.56         8.61         9.14        79.73        83.57         2.60 
TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A4ND 
       90.71        12.95        33.04        55.69        32.52        90.28 
TCGA-DD-A4NI TCGA-DD-A73B TCGA-DD-AACB TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACV 
       26.83         9.30        76.41        61.68        13.64        50.33 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADO TCGA-DD-AADP 
       44.22        22.09        40.08        40.47        14.89        15.06 
TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEK TCGA-ED-A7PZ 
       18.25        18.61         4.64        25.08        35.08         0.20 
TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A496 TCGA-FV-A4ZP 
       14.04         1.84         0.62        23.97         0.33        81.73 
TCGA-G3-A25S TCGA-G3-A5SJ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV6 TCGA-KR-A7K2 
       13.68        22.95        11.80        12.23         2.14        21.60 
TCGA-KR-A7K7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
       31.27        19.33        19.04        36.10        17.59        16.44 
TCGA-UB-A7MF TCGA-YA-A8S7 
        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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        22.92         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 
       17.10         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        23.38         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         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC 
        3.19         3.39         3.32         9.96        10.36        11.41 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        8.94         7.13        21.34         9.83        12.00        13.12 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 
        4.60        11.31         9.17         6.94         8.15        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        26.63        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       79.07        89.69        82.62        59.93        72.39        80.71 
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        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         9.73         0.20        12.82        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-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        60.89        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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 
       25.25        20.42        17.10        22.06        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV3 
       11.87        14.14         1.84        15.78        15.65        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        29.79        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        22.95        24.56        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        17.69        21.01         3.09        21.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       15.39        15.52         0.76        19.76         1.71        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       10.75        10.32        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       24.85        18.28        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       35.87         0.69        25.15        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.20               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             90.71             120.82 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            17.920             20.055 
[1] "0.2 - 90.7 (17.9)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.1"
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     143       71         3         41          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                143
  STAGE II                 14                 71
  STAGE III                 0                  3
  STAGE IIIA               19                 41
  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   152  75  52  11
D63V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               30                152
  T2                  17                 75
  T3                  22                 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"
D63V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    51   2
  11Q LOSS WILD-TYPE 199   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     51    2
  11Q LOSS WILD-TYPE  199    1
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               51                199
  1                2                  1
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    55   1
  11Q LOSS WILD-TYPE 206   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     55    1
  11Q LOSS WILD-TYPE  206    3
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               55                206
  1                1                  3
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    22  48
  11Q LOSS WILD-TYPE  93 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     22   48
  11Q LOSS WILD-TYPE   93  199
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               22                 93
  MALE                 48                199
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    65   1
  11Q LOSS WILD-TYPE 271   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     65    1
  11Q LOSS WILD-TYPE  271    6
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                65                271
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11Q LOSS MUTATED                         1                       66
  11Q LOSS WILD-TYPE                       1                      287
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11Q LOSS MUTATED                                  3
  11Q LOSS WILD-TYPE                                4
D63V9, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       66                287
  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 257  10   1  17
D63V10, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               61                257
  R1                5                 10
  R2                0                  1
  RX                4                 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
  11Q LOSS MUTATED                                  0    31
  11Q LOSS WILD-TYPE                                1   126
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           4    35
  11Q LOSS WILD-TYPE                        13   142
D63V11, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          31                126
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          35                142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     5  61
  11Q LOSS WILD-TYPE   8 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      5   61
  11Q LOSS WILD-TYPE    8  271
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  8
  NOT HISPANIC OR LATINO               61                271
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    37  22
  12P LOSS WILD-TYPE 192 107
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                59                299 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                22                107 
$`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        45.93        17.98        44.81 
TCGA-CC-A1HT TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HV 
        3.32        11.93         8.94         8.61         9.14         9.17 
TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
        7.33        45.11        49.15        33.04        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
        5.62         7.66        33.14        30.15        26.83        30.51 
TCGA-DD-A4NO TCGA-DD-A73F TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACU 
       73.81        35.67        63.48        15.42        42.81        51.52 
TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AAE3 
       47.67        44.22        40.08         0.39        14.89        18.61 
TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVV 
       26.63        50.33        35.08        79.07        72.39        80.71 
TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A496 
       13.15         0.20         0.62         8.12         6.38         0.33 
TCGA-G3-A25S TCGA-G3-A25Z TCGA-G3-A7M6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-MI-A75G 
       13.68        21.53        20.78        11.87         1.02        22.95 
TCGA-MI-A75I TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-AA0U TCGA-ZP-A9D1 
       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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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        17.10        14.76 
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        23.38         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         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 
        2.86         3.19         3.39         4.24         3.35         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF 
        9.96        10.36        11.41         9.99         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HU 
        9.83        12.00        13.12        12.56         4.60        11.31 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
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-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-A4NK 
        0.36        30.61        32.52        90.28        30.97        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
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-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       55.40        12.53        12.00         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        0.30         3.52        58.16        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       59.31        51.35        50.33        46.82         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA 
        4.50        18.54        21.63        42.58        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-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP 
       35.67        35.05        34.49        20.91        29.52        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-AAEG TCGA-DD-AAEH TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       23.64        25.78        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        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E 
        9.73         0.20        12.82         0.20        14.04        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-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-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       19.10        27.88        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-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-A7M5 TCGA-G3-A7M7 
       22.95        20.42        17.10        22.06        14.70        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       14.14         1.84        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A9DB 
       13.55         0.89         8.75         2.14        22.92         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        24.56         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.33        19.04        15.39        36.10        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       16.44         1.71        15.98         7.04        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
        0.99        12.99        20.22        24.85        18.28        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
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 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.20               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             80.71             120.82 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             18.61              19.76 
[1] "0.2 - 80.7 (18.6)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED        24       16         1          8          3
  12P LOSS WILD-TYPE     147       69         2         52          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                147
  STAGE II                 16                 69
  STAGE III                 1                  2
  STAGE IIIA                8                 52
  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  21  12   1
  12P LOSS WILD-TYPE   155  71  62  11
D64V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1               27                155
  T2                  21                 71
  T3                  12                 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"
D64V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    41   2
  12P LOSS WILD-TYPE 209   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     41    2
  12P LOSS WILD-TYPE  209    1
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               41                209
  1                2                  1
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    47   2
  12P LOSS WILD-TYPE 214   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     47    2
  12P LOSS WILD-TYPE  214    2
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               47                214
  1                2                  2
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    17  44
  12P LOSS WILD-TYPE  98 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     17   44
  12P LOSS WILD-TYPE   98  203
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               17                 98
  MALE                 44                203
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    57   0
  12P LOSS WILD-TYPE 279   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     57    0
  12P LOSS WILD-TYPE  279    7
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                57                279
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12P LOSS MUTATED                         0                       60
  12P LOSS WILD-TYPE                       2                      293
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12P LOSS MUTATED                                  1
  12P LOSS WILD-TYPE                                6
D64V9, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       60                293
  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    52   3   1   4
  12P LOSS WILD-TYPE 266  12   0  17
D64V10, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               52                266
  R1                3                 12
  R2                1                  0
  RX                4                 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
  12P LOSS MUTATED                                  0    30
  12P LOSS WILD-TYPE                                1   127
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           4    25
  12P LOSS WILD-TYPE                        13   152
D64V11, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          30                127
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          25                152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3  55
  12P LOSS WILD-TYPE  10 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3   55
  12P LOSS WILD-TYPE   10  277
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               55                277
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    17  14
  12Q LOSS WILD-TYPE 212 115
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                327 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                14                115 
$`12Q LOSS MUTATED`
TCGA-2Y-A9GS TCGA-3K-AAZ8 TCGA-BC-A217 TCGA-CC-A1HT TCGA-CC-A3MC TCGA-CC-A5UE 
       23.80        13.02        45.93         3.32        11.93         8.94 
TCGA-CC-A7IL TCGA-CC-A8HV TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL 
        9.14         9.17         7.33        45.11        49.15        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-AACE TCGA-DD-AACG 
       55.69         5.62        26.83        73.81        63.48        15.42 
TCGA-DD-AACN TCGA-DD-AACU TCGA-DD-AAD8 TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVU 
       42.81        51.52        40.08        18.61        35.08        72.39 
TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A25Z TCGA-MI-A75G 
        0.20         0.62         8.12         0.33        21.53        22.95 
TCGA-ZP-A9D1 
        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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       14.76         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        23.38 
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         4.24         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC 
        4.24         3.35         9.86         9.96        10.36        11.41 
TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        9.99         7.13        21.34         9.83        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW 
       12.56         8.61         4.60        11.31         6.94         8.15 
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-A1EI TCGA-DD-A1EJ 
       19.79        75.65        11.47        12.95         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        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-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-A4NP 
       30.15        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-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-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-AACS TCGA-DD-AACT 
       58.16        61.68        13.64        14.20        59.31        51.35 
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-AADA 
       18.54        21.63        42.58        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-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        26.63        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        80.71        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        29.92        26.93        28.08        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-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41        13.35         1.84        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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10        27.88         6.38        12.03         0.03 
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-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        58.49        14.86        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       22.06        14.70        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        8.75         2.14        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        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        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        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        36.10 
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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.20               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             73.81             120.82 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             18.61              19.76 
[1] "0.2 - 73.8 (18.6)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
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     159       76         2         55          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                159
  STAGE II                  9                 76
  STAGE III                 1                  2
  STAGE IIIA                5                 55
  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   169  81  66  11
D65V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               13                169
  T2                  11                 81
  T3                   8                 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"
D65V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    24   0
  12Q LOSS WILD-TYPE 226   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     24    0
  12Q LOSS WILD-TYPE  226    3
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               24                226
  1                0                  3
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    26   2
  12Q LOSS WILD-TYPE 235   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     26    2
  12Q LOSS WILD-TYPE  235    2
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               26                235
  1                2                  2
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     9  24
  12Q LOSS WILD-TYPE 106 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      9   24
  12Q LOSS WILD-TYPE  106  223
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                9                106
  MALE                 24                223
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    30   0
  12Q LOSS WILD-TYPE 306   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     30    0
  12Q LOSS WILD-TYPE  306    7
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                30                306
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12Q LOSS MUTATED                         0                       32
  12Q LOSS WILD-TYPE                       2                      321
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12Q LOSS MUTATED                                  1
  12Q LOSS WILD-TYPE                                6
D65V9, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       32                321
  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 289  15   0  19
D65V10, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               29                289
  R1                0                 15
  R2                1                  0
  RX                2                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   139
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           3    12
  12Q LOSS WILD-TYPE                        14   165
D65V11, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          18                139
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          12                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"
D65V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2  30
  12Q LOSS WILD-TYPE  11 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   30
  12Q LOSS WILD-TYPE   11  302
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               30                302
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    69  47
  13Q LOSS WILD-TYPE 160  82
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               116                242 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                47                 82 
$`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        45.93        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-5264 
        0.66         4.24         2.86         3.19         3.39         3.35 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IJ TCGA-CC-A7IK 
        9.86         9.96        11.41         8.94        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        9.14         9.17         6.94        79.73        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK 
      113.00         2.60        21.76        12.95         6.02        18.35 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NA 
       55.69         5.62        25.81       102.74        30.61        33.14 
TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-A73G 
       30.15        29.56        73.81        12.26        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       13.48        15.42        53.19         3.52        58.16        42.81 
TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AAD1 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD 
       13.64        59.31        18.54        40.08        13.97        40.47 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADR 
        3.78        35.67        34.49         0.39        14.89        66.67 
TCGA-DD-AAE0 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVQ 
       18.25        21.83        25.08        23.64        35.08        89.69 
TCGA-DD-AAVV TCGA-ED-A4XI TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       80.71        26.93         0.20         0.20        14.04        13.15 
TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X 
       11.93        27.88         6.38        13.68        51.06        58.49 
TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-AAV4 TCGA-G3-AAV7 
       25.64        17.10        14.70        20.78         0.89        11.87 
TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-MI-A75G TCGA-MI-A75I 
       22.92         2.20        17.06        21.60        22.95        20.71 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       10.85        26.27        21.01        19.04        15.39        15.52 
TCGA-UB-A7MA TCGA-UB-AA0U TCGA-WJ-A86L TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY 
       17.59        10.75        11.34        22.78        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        49.84        47.74        11.74        38.40 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AA1C 
       22.92         1.18         8.55         8.61         0.66        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U 
       14.76         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        23.38         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-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       10.36        11.93         9.99         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A114 
       12.00        13.12         4.60        11.31         8.15        37.78 
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-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ 
       19.79        75.65        11.47        45.11        49.15        33.04 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        27.19        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB 
       17.59        20.12       107.11        13.78         0.36        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       90.28        30.97        26.83        30.51        39.78        56.25 
TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
      108.76         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       23.05        22.78         1.45         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-AACJ TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU 
       69.11         0.30        61.68        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-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        42.58        44.22        22.09        40.54        40.83 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP 
       39.52        37.64        35.05        20.91        29.52        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-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-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        18.90        15.72        26.63        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.07        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-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       29.92        28.08        13.91        13.35         9.73        12.82 
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-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
       20.61        19.59         0.62         9.96        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10         8.12        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-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-A6UC TCGA-G3-A7M7 TCGA-G3-A7M8 
       25.25        22.95        20.42        22.06        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        8.75         2.14         1.02         2.99        37.71        20.75 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       16.83        11.80         2.14        31.27        29.79        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        24.56         7.53 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RG-A7D4 
       58.88        17.69         3.09        21.04        19.33        36.10 
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-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.32         0.99        12.99        20.22        24.85        18.28 
TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        23.21        35.87         0.69        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF 
       45.57        79.30 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.20               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            114.35             120.82 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             18.25              20.17 
[1] "0.2 - 114.3 (18.2)" "0.0 - 120.8 (20.2)"
[1] "hr=" "1.3"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED        47       35         1         17          4
  13Q LOSS WILD-TYPE     124       50         2         43          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                  47                124
  STAGE II                 35                 50
  STAGE III                 1                  2
  STAGE IIIA               17                 43
  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      49  38  22   9
  13Q LOSS WILD-TYPE   133  54  52   3
D66V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               49                133
  T2                  38                 54
  T3                  22                 52
  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    82   1
  13Q LOSS WILD-TYPE 168   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     82    1
  13Q LOSS WILD-TYPE  168    2
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               82                168
  1                1                  2
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    85   2
  13Q LOSS WILD-TYPE 176   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     85    2
  13Q LOSS WILD-TYPE  176    2
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               85                176
  1                2                  2
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    44  74
  13Q LOSS WILD-TYPE  71 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     44   74
  13Q LOSS WILD-TYPE   71  173
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               44                 71
  MALE                 74                173
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   111   1
  13Q LOSS WILD-TYPE 225   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    111    1
  13Q LOSS WILD-TYPE  225    6
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               111                225
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  13Q LOSS MUTATED                         1                      113
  13Q LOSS WILD-TYPE                       1                      240
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  13Q LOSS MUTATED                                  4
  13Q LOSS WILD-TYPE                                3
D66V9, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                      113                240
  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    97   8   0  10
  13Q LOSS WILD-TYPE 221   7   1  11
D66V10, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               97                221
  R1                8                  7
  R2                0                  1
  RX               10                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0    55
  13Q LOSS WILD-TYPE                                1   102
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           5    58
  13Q LOSS WILD-TYPE                        12   119
D66V11, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          55                102
  BLACK OR AFRICAN AMERICAN                       5                 12
  WHITE                                          58                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"
D66V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4 110
  13Q LOSS WILD-TYPE   9 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4  110
  13Q LOSS WILD-TYPE    9  222
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  9
  NOT HISPANIC OR LATINO              110                222
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    58  45
  14Q LOSS WILD-TYPE 171  84
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               103                255 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                45                 84 
$`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        49.84        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        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5264 
        0.26        22.36         4.24         2.86         3.19         3.35 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE 
        3.32         9.96        10.36        11.93         8.94         7.13 
TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU 
        9.83        13.12        12.56         8.61         4.60        11.31 
TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C 
        9.17        79.73        83.57       113.00         2.60        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       90.71        45.11        33.04        13.64        55.69         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI 
        7.66        13.78        30.61        32.52        30.15        26.83 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-AA3A TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACN 
       73.81        12.26        13.48        63.48        15.42        42.81 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB 
       59.31        51.52         5.62        44.22        22.09        40.83 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       40.47         3.78        20.91         0.39        29.52        14.89 
TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAEE TCGA-DD-AAEG 
       66.67        18.87        19.30        18.25        26.63        23.64 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ 
       72.39        80.71        53.69        29.92         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A4ZP 
       13.41         1.84         0.20        19.59        11.93        81.73 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 
       13.68        58.49        25.64        17.10         1.84        11.80 
TCGA-G3-AAV7 TCGA-K7-A5RG TCGA-KR-A7K7 TCGA-NI-A8LF TCGA-RC-A7SF TCGA-RC-A7SH 
       11.87        17.06        31.27        26.27        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.52        36.10        16.44         0.99        12.99        20.22 
TCGA-ZP-A9D2 
       25.15 

$`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        38.40        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VH 
       22.92         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 
       17.10        14.76         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        23.38         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         9.86 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A9FS 
       11.41         9.99        21.34        12.00         9.14         6.94 
TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
        8.15        37.78        53.33         7.33         0.46        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-A39Z 
       49.15         6.02        18.35        21.14        27.19        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK 
        0.36        33.14        90.28        30.97        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       56.25        29.56       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-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-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT 
        3.52        58.16        61.68        13.64        14.20        51.35 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 
       50.33        46.82         5.59        47.67         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADE 
       21.63        42.58        40.08        40.54        13.97        39.52 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADP TCGA-DD-AADQ 
       37.64        35.67        35.05        34.49        15.06        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       15.58        18.21        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-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       15.72        25.08        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-ED-A4XI TCGA-ED-A5KG 
       62.47        66.25        65.39        49.48        26.93        28.08 
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-A2KC TCGA-EP-A3JL 
       13.35        18.74        19.99        20.61         0.62         9.96 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        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-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.78        15.65        12.23        13.55         0.89         8.75 
TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14        22.92         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 
       20.75        16.83        11.80         2.14        21.60        29.79 
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        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       24.56        20.71         7.53        10.85        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-T1-A6J8 TCGA-UB-A7MA 
       21.01         3.09        21.04        19.33         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-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       11.34        24.85        18.28        22.78        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        35.87         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 
              0.20               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            113.00             120.82 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             18.25              20.12 
[1] "0.2 - 113.0 (18.2)" "0.0 - 120.8 (20.1)"
[1] "hr=" "1.4"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED        38       30         0         22          4
  14Q LOSS WILD-TYPE     133       55         3         38          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                  38                133
  STAGE II                 30                 55
  STAGE III                 0                  3
  STAGE IIIA               22                 38
  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      39  34  28   5
  14Q LOSS WILD-TYPE   143  58  46   7
D67V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1               39                143
  T2                  34                 58
  T3                  28                 46
  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    76   1
  14Q LOSS WILD-TYPE 174   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     76    1
  14Q LOSS WILD-TYPE  174    2
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               76                174
  1                1                  2
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    84   2
  14Q LOSS WILD-TYPE 177   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     84    2
  14Q LOSS WILD-TYPE  177    2
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               84                177
  1                2                  2
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    29  77
  14Q LOSS WILD-TYPE  86 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     29   77
  14Q LOSS WILD-TYPE   86  170
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               29                 86
  MALE                 77                170
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    99   2
  14Q LOSS WILD-TYPE 237   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     99    2
  14Q LOSS WILD-TYPE  237    5
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                99                237
  YES                2                  5
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  14Q LOSS MUTATED                         1                      102
  14Q LOSS WILD-TYPE                       1                      251
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  14Q LOSS MUTATED                                  3
  14Q LOSS WILD-TYPE                                4
D67V9, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                      102                251
  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    91   5   0   8
  14Q LOSS WILD-TYPE 227  10   1  13
D67V10, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               91                227
  R1                5                 10
  R2                0                  1
  RX                8                 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
  14Q LOSS MUTATED                                  0    57
  14Q LOSS WILD-TYPE                                1   100
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           4    43
  14Q LOSS WILD-TYPE                        13   134
D67V11, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          57                100
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          43                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"
D67V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     5  95
  14Q LOSS WILD-TYPE   8 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5   95
  14Q LOSS WILD-TYPE    8  237
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  8
  NOT HISPANIC OR LATINO               95                237
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    32  31
  15Q LOSS WILD-TYPE 197  98
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                63                295 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                31                 98 
$`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-5264 TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IG 
        4.24         3.35         9.96        11.41         9.99         9.83 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 
       13.12        12.56         8.61         9.17         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EI TCGA-DD-A1EJ 
       37.78        83.57         2.60        90.71         6.02        33.04 
TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A4NA TCGA-DD-A4NQ TCGA-DD-A73B 
       13.64         5.62       102.74        33.14        12.26         9.30 
TCGA-DD-AAC8 TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AADB TCGA-DD-AADK TCGA-DD-AADO 
        0.53        15.42         3.52        40.83        34.49        14.89 
TCGA-DD-AAE1 TCGA-DD-AAVQ TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX 
       18.15        89.69        80.71        29.92         9.73         0.20 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KB TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25Z 
        0.20        13.41        19.59         0.33        81.73        21.53 
TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       17.10         1.84        11.80         0.89         2.14        11.87 
TCGA-GJ-A3OU TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-RG-A7D4 TCGA-UB-A7MA 
       22.92        17.06        21.60        31.27        36.10        17.59 
TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CF 
        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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       47.74        18.25        11.74        38.40        22.92         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        17.10        14.76 
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        23.38         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I 
       69.57        44.42        45.93         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         9.86        10.36 
TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IL 
       11.93         8.94         7.13        21.34        12.00         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        4.60        11.31         6.94        53.33       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK 
       75.65        11.47        12.95        45.11        49.15        18.35 
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-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       70.06        17.59        20.12       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        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-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-AAC9 TCGA-DD-AACA 
        1.45        35.67       114.35        13.48        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-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-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-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-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       35.05        20.91         0.39        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-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        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        26.63 
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-A4XI TCGA-ED-A5KG 
       66.25        65.39        49.48        53.69        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
       13.91        13.35        12.82        14.04        13.15        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-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-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M5 
       19.23        25.25        22.95        20.42        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       20.78        11.87        14.14        15.78        15.65        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       13.55         8.75         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG 
       20.75        16.83        11.80         2.14        29.79        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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        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-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       15.52         0.76        19.76        16.44         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 
        7.04        10.75        10.32        11.34        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       24.85        18.28        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       35.87         0.69        25.15        12.99        45.57        40.80 
TCGA-ZS-A9CG 
       11.21 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.20               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            102.74             120.82 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             13.41              20.91 
[1] "0.2 - 102.7 (13.4)" "0.0 - 120.8 (20.9)"
[1] "hr=" "1.8"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  15Q LOSS MUTATED        20       22         1         15          2
  15Q LOSS WILD-TYPE     151       63         2         45          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                  20                151
  STAGE II                 22                 63
  STAGE III                 1                  2
  STAGE IIIA               15                 45
  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      22  22  20   1
  15Q LOSS WILD-TYPE   160  70  54  11
D68V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1               22                160
  T2                  22                 70
  T3                  20                 54
  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    44   2
  15Q LOSS WILD-TYPE 206   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     44    2
  15Q LOSS WILD-TYPE  206    1
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               44                206
  1                2                  1
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    55   0
  15Q LOSS WILD-TYPE 206   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     55    0
  15Q LOSS WILD-TYPE  206    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               55                206
  1                0                  4
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    20  45
  15Q LOSS WILD-TYPE  95 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     20   45
  15Q LOSS WILD-TYPE   95  202
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               20                 95
  MALE                 45                202
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    59   1
  15Q LOSS WILD-TYPE 277   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     59    1
  15Q LOSS WILD-TYPE  277    6
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                59                277
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  15Q LOSS MUTATED                         0                       63
  15Q LOSS WILD-TYPE                       2                      290
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  15Q LOSS MUTATED                                  2
  15Q LOSS WILD-TYPE                                5
D68V9, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       63                290
  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    57   3   0   5
  15Q LOSS WILD-TYPE 261  12   1  16
D68V10, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               57                261
  R1                3                 12
  R2                0                  1
  RX                5                 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
  15Q LOSS MUTATED                                  0    31
  15Q LOSS WILD-TYPE                                1   126
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           6    28
  15Q LOSS WILD-TYPE                        11   149
D68V11, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          31                126
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          28                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"
D68V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3  59
  15Q LOSS WILD-TYPE  10 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3   59
  15Q LOSS WILD-TYPE   10  273
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               59                273
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    64  42
  16P LOSS WILD-TYPE 165  87
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               106                252 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                42                 87 
$`16P LOSS MUTATED`
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-BC-A217 TCGA-BC-A5W4 
       56.91        49.84        38.40        20.81        45.93        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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.39         3.35         9.86        10.36        11.93        11.41 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HV 
        8.94         7.13        13.12        12.56         4.60         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EH 
        6.94         8.15        37.78         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-AACG TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
        9.30        55.40        15.42         3.52        58.16        42.81 
TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD3 
       13.64        59.31        51.52        46.82         5.62        42.58 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADO 
       40.54        40.83        35.67        35.05        20.91        14.89 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.06        66.67        19.30        18.25        18.25        18.15 
TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVU 
        4.64        21.83        25.08        35.08        59.93        72.39 
TCGA-DD-AAVZ TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O5 
       62.47        28.08        13.35         9.73        12.82        13.35 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 
        1.84        19.59        22.85        60.89        23.97        27.88 
TCGA-FV-A3R2 TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A7M5 TCGA-G3-A7M9 TCGA-G3-AAV6 
        6.38        58.49        14.86        14.70         1.84         2.14 
TCGA-G3-AAV7 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-QA-A7B7 TCGA-RC-A7SB 
       11.87        31.27        22.95        20.71         3.09        19.33 
TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MF TCGA-WQ-A9G7 
       15.39        36.10         0.76        17.59         7.04         0.99 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZS-A9CG 
       22.78        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        22.92         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        17.10        14.76         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        23.38         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-CC-A5UD 
       44.81        36.66         4.24         3.32         9.96         9.99 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU 
       21.34         9.83        12.00         8.61         9.14        11.31 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       75.65        11.47        45.11        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        55.69        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR 
       30.97        30.51        39.78        56.25       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        23.93        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-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       76.41        12.53        63.48        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACV 
       69.11         0.30        61.68        14.20        51.35        50.33 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 
        5.59        47.67         4.50        18.54        21.63        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       22.09        40.08        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS 
       37.64        34.49         0.39        29.52        14.33        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 
       18.21        18.87        20.98        18.61        19.99        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       23.74        18.90        15.72        26.63        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVV TCGA-DD-AAVW 
       50.33        79.07        89.69        82.62        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        64.77        66.25        65.39        49.48        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO 
       29.92        26.93        13.91         0.20         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.15        13.41         0.20        18.74        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 
        0.62         9.96        11.93        14.40        19.10         8.12 
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-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-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        22.06        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75        22.92         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83        11.80         2.14        21.60 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       29.79        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       24.56         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MC 
       21.01        21.04        19.04        15.52        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
        1.71        15.98        10.75        10.32        11.34        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       20.22        24.85        18.28        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.87        25.15        12.99        45.57        40.80        79.30 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.36               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             90.28             120.82 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            16.505             20.765 
[1] "0.4 - 90.3 (16.5)"  "0.0 - 120.8 (20.8)"
[1] "hr=" "1.4"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P LOSS MUTATED        43       32         1         20          3
  16P LOSS WILD-TYPE     128       53         2         40          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                  43                128
  STAGE II                 32                 53
  STAGE III                 1                  2
  STAGE IIIA               20                 40
  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      48  33  24   4
  16P LOSS WILD-TYPE   134  59  50   8
D69V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1               48                134
  T2                  33                 59
  T3                  24                 50
  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 169   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     81    2
  16P LOSS WILD-TYPE  169    1
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               81                169
  1                2                  1
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    88   2
  16P LOSS WILD-TYPE 173   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     88    2
  16P LOSS WILD-TYPE  173    2
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               88                173
  1                2                  2
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    39  70
  16P LOSS WILD-TYPE  76 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     39   70
  16P LOSS WILD-TYPE   76  177
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               39                 76
  MALE                 70                177
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   101   0
  16P LOSS WILD-TYPE 235   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    101    0
  16P LOSS WILD-TYPE  235    7
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO               101                235
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16P LOSS MUTATED                         0                      107
  16P LOSS WILD-TYPE                       2                      246
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16P LOSS MUTATED                                  2
  16P LOSS WILD-TYPE                                5
D69V9, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                      107                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
  16P LOSS MUTATED    96   2   0  10
  16P LOSS WILD-TYPE 222  13   1  11
D69V10, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               96                222
  R1                2                 13
  R2                0                  1
  RX               10                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0    62
  16P LOSS WILD-TYPE                                1    95
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           6    40
  16P LOSS WILD-TYPE                        11   137
D69V11, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          62                 95
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          40                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"
D69V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     6 100
  16P LOSS WILD-TYPE   7 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      6  100
  16P LOSS WILD-TYPE    7  232
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  7
  NOT HISPANIC OR LATINO              100                232
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    86  55
  16Q LOSS WILD-TYPE 143  74
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               141                217 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                55                 74 
$`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        49.84        18.25        38.40        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        45.93 
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         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3MB TCGA-CC-A3MC 
        2.86         3.19         4.24         3.35        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        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        29.92        28.08        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-A7M5 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV6 
       25.64        25.25        14.70         1.84        15.78         2.14 
TCGA-G3-AAV7 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-O8-A75V TCGA-QA-A7B7 
       11.87        31.27        22.95        20.71        17.69         3.09 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.33        19.04        15.39        36.10         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-XR-A8TF 
       19.76         7.04        10.75        11.34         0.99        22.78 
TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CG 
       23.21         0.69        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        22.92 
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        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       14.76         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        23.38         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-CC-A7IH TCGA-CC-A7II 
        3.39         3.32         9.86         9.96        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 
       12.56         8.61         9.14        83.57       113.00         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-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       75.65        11.47        45.11        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        55.69        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR 
       30.97        30.51        39.78        56.25       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        23.93        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-AACD TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACT 
       76.41        12.53        63.48        69.11         0.30        51.35 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD5 
       50.33         5.59        47.67         4.50        21.63        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       22.09        40.08        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV 
       37.64        29.52        14.33        15.58        18.21        18.87 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA 
       20.98        18.61        19.99        21.17        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR 
       15.72        26.63        23.64        50.33        79.07        82.62 
TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       80.71        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 
       26.93        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        22.06        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75        22.92         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83        11.80         2.14        21.60 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       29.79        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF 
       24.56         7.53        10.85        58.88        26.27        21.01 
TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V 
       21.04        15.52        16.44         1.71        15.98        10.32 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       12.99        20.22        24.85        18.28        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       25.71        35.87        25.15        12.99        45.57        40.80 
TCGA-ZS-A9CF 
       79.30 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.36               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             90.28             120.82 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             18.48              20.61 
[1] "0.4 - 90.3 (18.5)"  "0.0 - 120.8 (20.6)"
[1] "hr=" "1.4"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED        58       46         1         23          3
  16Q LOSS WILD-TYPE     113       39         2         37          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                  58                113
  STAGE II                 46                 39
  STAGE III                 1                  2
  STAGE IIIA               23                 37
  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      64  47  28   5
  16Q LOSS WILD-TYPE   118  45  46   7
D70V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               64                118
  T2                  47                 45
  T3                  28                 46
  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 143   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    107    2
  16Q LOSS WILD-TYPE  143    1
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              107                143
  1                2                  1
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   114   2
  16Q LOSS WILD-TYPE 147   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    114    2
  16Q LOSS WILD-TYPE  147    2
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              114                147
  1                2                  2
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    50  94
  16Q LOSS WILD-TYPE  65 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     50   94
  16Q LOSS WILD-TYPE   65  153
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               50                 65
  MALE                 94                153
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   133   2
  16Q LOSS WILD-TYPE 203   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    133    2
  16Q LOSS WILD-TYPE  203    5
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               133                203
  YES                2                  5
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16Q LOSS MUTATED                         0                      141
  16Q LOSS WILD-TYPE                       2                      212
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16Q LOSS MUTATED                                  3
  16Q LOSS WILD-TYPE                                4
D70V9, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                      141                212
  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   127   6   0  11
  16Q LOSS WILD-TYPE 191   9   1  10
D70V10, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0              127                191
  R1                6                  9
  R2                0                  1
  RX               11                 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
  16Q LOSS MUTATED                                  0    84
  16Q LOSS WILD-TYPE                                1    73
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           7    50
  16Q LOSS WILD-TYPE                        10   127
D70V11, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          84                 73
  BLACK OR AFRICAN AMERICAN                       7                 10
  WHITE                                          50                127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     7 133
  16Q LOSS WILD-TYPE   6 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7  133
  16Q LOSS WILD-TYPE    6  199
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                  6
  NOT HISPANIC OR LATINO              133                199
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   101  75
  17P LOSS WILD-TYPE 128  54
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               176                182 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                75                 54 
$`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        22.92         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        23.38 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57         5.03        45.93         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         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT 
        2.86         3.19         3.39         4.24         3.35         3.32 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF 
       10.36        11.93        11.41         9.99         8.94        21.34 
TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       13.12         8.61         9.14         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        6.94        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        26.63        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A7PX 
       82.62        72.39        80.71        65.39        29.92         0.20 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A23B 
        0.20        13.41         1.84         0.20         0.62        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25U 
       23.97        19.10        27.88         0.03        13.68        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SL TCGA-G3-A5SM 
       28.27        14.86        21.53        25.64        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 
       14.70        20.78         1.84        15.78        11.80         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-AAU7 
        8.75        11.87        22.92         1.02        37.71        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
        2.14        21.60        12.72        16.67        22.95        20.71 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SK TCGA-RG-A7D4 
       58.88        17.69         3.09        19.33        15.52        36.10 
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-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       11.34        12.99        13.55         0.69        25.15        12.99 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       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        49.84        47.74 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG 
       11.74        38.40         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        17.10        14.76        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-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ 
        9.86         9.96         7.13         9.83        12.00        12.56 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EC 
        8.15        79.73        37.78         0.46        90.71        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       75.65        11.47        12.95        21.14        27.19        55.69 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       19.76         7.66        70.06       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.61        90.28        30.97        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       73.81       108.76         0.30        80.75        78.84        23.93 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05        22.78        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACK 
       11.41        76.41        12.53        12.00        53.19         0.30 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       42.81        61.68        13.64        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD5 
       50.33        46.82        47.67         4.50        21.63        44.22 
TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
       40.54        40.47        35.67        35.05        34.49         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE1 
       14.89        15.06        14.33        15.58        18.21        18.15 
TCGA-DD-AAE3 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAED TCGA-DD-AAEG 
       18.61        21.17        21.83        23.74        25.08        23.64 
TCGA-DD-AAEH TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       25.78        59.93        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       66.25        49.48        53.69        26.93        28.08        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-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-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 
       22.85        14.40         8.12         6.38        12.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG 
       81.73         0.39        51.06        30.74        58.49        22.13 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A6UC 
        5.92        19.53        19.23        25.25        22.95        22.06 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 
       11.87        14.14        15.65        12.23        13.55         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        31.27 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H TCGA-MR-A520 
       29.79        13.97        12.03         9.57        24.56         7.53 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
       10.85        26.27        21.01        21.04        19.04        15.39 
TCGA-UB-A7MA TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 
       17.59        10.75        10.32         0.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       18.28        22.78        35.77        25.71        23.21        35.87 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       45.57        11.21 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            120.82             114.35 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            18.510             21.025 
[1] "0.0 - 120.8 (18.5)" "0.3 - 114.3 (21.0)"
[1] "hr=" "1.6"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED        68       49         2         33          3
  17P LOSS WILD-TYPE     103       36         1         27          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                  68                103
  STAGE II                 49                 36
  STAGE III                 2                  1
  STAGE IIIA               33                 27
  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      75  55  40   8
  17P LOSS WILD-TYPE   107  37  34   4
D71V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               75                107
  T2                  55                 37
  T3                  40                 34
  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   124   3
  17P LOSS WILD-TYPE 126   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    124    3
  17P LOSS WILD-TYPE  126    0
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              124                126
  1                3                  0
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   132   3
  17P LOSS WILD-TYPE 129   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    132    3
  17P LOSS WILD-TYPE  129    1
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              132                129
  1                3                  1
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    57 122
  17P LOSS WILD-TYPE  58 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     57  122
  17P LOSS WILD-TYPE   58  125
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               57                 58
  MALE                122                125
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   167   3
  17P LOSS WILD-TYPE 169   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    167    3
  17P LOSS WILD-TYPE  169    4
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               167                169
  YES                3                  4
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17P LOSS MUTATED                         1                      173
  17P LOSS WILD-TYPE                       1                      180
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17P LOSS MUTATED                                  5
  17P LOSS WILD-TYPE                                2
D71V9, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                      173                180
  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   155   7   1  14
  17P LOSS WILD-TYPE 163   8   0   7
D71V10, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              155                163
  R1                7                  8
  R2                1                  0
  RX               14                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0    85
  17P LOSS WILD-TYPE                                1    72
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           9    81
  17P LOSS WILD-TYPE                         8    96
D71V11, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          85                 72
  BLACK OR AFRICAN AMERICAN                       9                  8
  WHITE                                          81                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     8 163
  17P LOSS WILD-TYPE   5 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      8  163
  17P LOSS WILD-TYPE    5  169
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  5
  NOT HISPANIC OR LATINO              163                169
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    20  15
  17Q LOSS WILD-TYPE 209 114
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                35                323 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                15                114 
$`17Q LOSS MUTATED`
TCGA-2Y-A9GZ TCGA-2Y-A9H5 TCGA-BC-A10R TCGA-BC-A5W4 TCGA-BD-A3EP TCGA-CC-A7II 
       27.88        18.25        10.13        17.98        13.45        13.12 
TCGA-CC-A7IL TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A3A0 TCGA-DD-A4NB 
        9.14        66.31        45.11        33.04        25.81        32.52 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-AACH TCGA-DD-AACZ TCGA-DD-AAE0 
       30.15        26.83        30.51         6.41         5.62        18.25 
TCGA-DD-AAEK TCGA-ED-A82E TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A5SL 
       35.08        13.41         0.20        23.97        27.88        20.42 
TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-RG-A7D4 
       17.10         1.84        11.80         2.14        21.60        36.10 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 
        0.76         7.04        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        49.84        47.74 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        38.40        20.81        22.92         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        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
       14.76         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        23.38         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        45.93         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-5264 
        4.24         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       12.56         8.61         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        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-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       79.40        19.79        75.65        11.47        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
        6.02        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       90.28        30.97        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-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-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-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 
       26.63        23.64        25.78        50.33        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        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 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
        0.20        12.82         0.20        14.04        13.15        13.35 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        1.84        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-A2QR 
        9.96        11.93        22.85        14.40        60.89        19.10 
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-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-A6UC TCGA-G3-A7M5 
       19.53        19.23        25.25        22.95        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       20.78        11.87        14.14        15.78        15.65        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89         8.75         2.14        11.87        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       16.83        11.80        31.27        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        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-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       17.59        19.76        16.44         1.71        15.98        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.32        11.34         0.99        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       22.78        35.77        25.71        23.21        35.87        25.15 
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 

  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              19.99 
[1] "0.2 - 66.3 (18.0)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.7"
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     162       75         3         51          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                162
  STAGE II                 10                 75
  STAGE III                 0                  3
  STAGE IIIA                9                 51
  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   169  81  62  11
D72V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1               13                169
  T2                  11                 81
  T3                  12                 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"
D72V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    22   2
  17Q LOSS WILD-TYPE 228   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     22    2
  17Q LOSS WILD-TYPE  228    1
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               22                228
  1                2                  1
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    28   1
  17Q LOSS WILD-TYPE 233   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     28    1
  17Q LOSS WILD-TYPE  233    3
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               28                233
  1                1                  3
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    15  22
  17Q LOSS WILD-TYPE 100 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     15   22
  17Q LOSS WILD-TYPE  100  225
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               15                100
  MALE                 22                225
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    35   0
  17Q LOSS WILD-TYPE 301   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     35    0
  17Q LOSS WILD-TYPE  301    7
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                35                301
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17Q LOSS MUTATED                         1                       33
  17Q LOSS WILD-TYPE                       1                      320
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17Q LOSS MUTATED                                  3
  17Q LOSS WILD-TYPE                                4
D72V9, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       33                320
  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 284  14   1  19
D72V10, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               34                284
  R1                1                 14
  R2                0                  1
  RX                2                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   147
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           2    24
  17Q LOSS WILD-TYPE                        15   153
D72V11, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          10                147
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          24                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"
D72V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2  32
  17Q LOSS WILD-TYPE  11 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   32
  17Q LOSS WILD-TYPE   11  300
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               32                300
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    44  26
  18P LOSS WILD-TYPE 185 103
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                70                288 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                26                103 
$`18P LOSS MUTATED`
TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-A10R TCGA-BC-A112 
       49.84        20.81         0.66        14.76        10.13         5.03 
TCGA-BC-A217 TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A7IK TCGA-CC-A8HV TCGA-DD-A118 
       45.93        10.36         9.99         8.61         9.17       113.00 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
        2.60         0.46        12.95        33.04        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A4 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73E 
        5.62        20.12        32.52        26.83        73.81         1.45 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
      114.35         0.53        76.41        55.40        12.53        63.48 
TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACZ 
       53.19        42.81        61.68        13.64        50.33         5.62 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADO TCGA-DD-AAE2 
       44.22        22.09        40.54        35.67        14.89        20.98 
TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7XP 
       23.64        35.08        80.71        29.92         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S 
       13.41         1.84        22.85        27.88         0.33        13.68 
TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MR-A8JO TCGA-NI-A8LF 
       11.80         2.14        31.27        22.95        10.85        26.27 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.52         0.76        17.59        19.76        16.44 
TCGA-WX-AA47 TCGA-YA-A8S7 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       18.28        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        38.40        22.92         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        17.10         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        23.38         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         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        3.19         3.39         4.24         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        9.96        11.93        11.41         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT 
        9.83        12.00        13.12        12.56         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
       11.31         6.94         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       53.33         7.33        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        11.47        45.11        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-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59       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-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-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACF 
       22.78        35.67        13.48        11.41        75.65        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42         6.41        69.11         0.30         3.52        58.16 
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-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 
       47.67         4.50        18.54        21.63        42.58        40.08 
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-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
       35.05        34.49        20.91         0.39        29.52        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-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.25        18.15        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-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       26.63        25.78        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-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        49.48        53.69        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.91        13.35         9.73        12.82         0.20        14.04 
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-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       19.10         8.12         6.38        12.03         0.03        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        25.25        22.95        20.42        17.10        22.06 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       14.70        20.78        11.87        14.14         1.84        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
       15.65        12.23        13.55         0.89         8.75        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 
       17.06        16.83        11.80         2.14        21.60        29.79 
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        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       20.71         7.53        58.88        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MD TCGA-UB-A7ME 
       21.04        19.33        15.39        36.10         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-AA44 TCGA-WX-AA46 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       20.22        24.85        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       35.87         0.69        25.15        12.99        45.57        79.30 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.20               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            114.35             120.82 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             18.66              19.89 
[1] "0.2 - 114.3 (18.7)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED        33       21         0         12          0
  18P LOSS WILD-TYPE     138       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                138
  STAGE II                 21                 64
  STAGE III                 0                  3
  STAGE IIIA               12                 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  21  14   1
  18P LOSS WILD-TYPE   146  71  60  11
D73V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               36                146
  T2                  21                 71
  T3                  14                 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    52   1
  18P LOSS WILD-TYPE 198   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     52    1
  18P LOSS WILD-TYPE  198    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               52                198
  1                1                  2
[1] 2 2
[1] FALSE
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    57   1
  18P LOSS WILD-TYPE 204   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     57    1
  18P LOSS WILD-TYPE  204    3
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               57                204
  1                1                  3
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    27  45
  18P LOSS WILD-TYPE  88 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     27   45
  18P LOSS WILD-TYPE   88  202
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               27                 88
  MALE                 45                202
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    63   3
  18P LOSS WILD-TYPE 273   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     63    3
  18P LOSS WILD-TYPE  273    4
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                63                273
  YES                3                  4
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18P LOSS MUTATED                         2                       67
  18P LOSS WILD-TYPE                       0                      286
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18P LOSS MUTATED                                  3
  18P LOSS WILD-TYPE                                4
D73V9, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       67                286
  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    65   2   0   5
  18P LOSS WILD-TYPE 253  13   1  16
D73V10, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               65                253
  R1                2                 13
  R2                0                  1
  RX                5                 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 LOSS MUTATED                                  0    34
  18P LOSS WILD-TYPE                                1   123
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           2    36
  18P LOSS WILD-TYPE                        15   141
D73V11, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          34                123
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          36                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"
D73V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  66
  18P LOSS WILD-TYPE  10 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   66
  18P LOSS WILD-TYPE   10  266
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               66                266
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    50  25
  18Q LOSS WILD-TYPE 179 104
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                75                283 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                25                104 
$`18Q LOSS MUTATED`
TCGA-2Y-A9H3 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-A10R TCGA-BC-A112 
       49.84        10.59         0.66        14.76        10.13         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A7IK TCGA-CC-A8HV 
       44.42        45.93        10.36         9.99         8.61         9.17 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL 
      113.00         2.60         0.46        12.95        33.04        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NO 
       55.69         5.62        30.61        32.52        26.83        73.81 
TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACE 
        9.30         1.45       114.35         0.53        76.41        63.48 
TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACX 
       53.19        42.81        61.68        13.64        50.33         5.59 
TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADO TCGA-DD-AADW 
        5.62        22.09        40.54        35.67        14.89        19.30 
TCGA-DD-AAE2 TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVV TCGA-ED-A459 
       20.98        23.64        35.08        79.07        80.71        29.92 
TCGA-ED-A66X TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A3I0 
       13.35        13.15        13.41         1.84        22.85        27.88 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-GJ-A3OU 
        0.33        13.68        14.70        11.80         2.14        22.92 
TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MR-A8JO TCGA-NI-A8LF TCGA-RC-A7SF TCGA-RC-A7SK 
       31.27        22.95        10.85        26.27        19.04        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MF TCGA-WX-AA44 TCGA-WX-AA47 
       36.10         0.76        16.44         7.04        20.22        18.28 
TCGA-YA-A8S7 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       13.55        40.80        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        38.40        20.81        22.92         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        17.10         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        23.38         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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.39         4.24         3.35         3.32         9.86         9.96 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.93        11.41         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       12.00        13.12        12.56         9.14         4.60        11.31 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        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-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
        0.36        33.14        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-A73C TCGA-DD-A73D TCGA-DD-A73F 
       80.75        78.84        23.93        23.05        22.78        35.67 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       13.48        11.41        75.65        55.40        12.53        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42         6.41        69.11         0.30         3.52        58.16 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACY 
       14.20        59.31        51.35        51.52        46.82        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-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-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
       35.05        34.49        20.91         0.39        29.52        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-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        18.15        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        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       25.78        50.33        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-A66Y 
       49.48        53.69        26.93        28.08        13.91         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20        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        22.06        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14         1.84        15.78        15.65        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        0.89         8.75        11.87         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       21.60        29.79        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V 
       16.67        24.56        20.71         7.53        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-UB-A7MA 
       21.01         3.09        21.04        19.33        15.39        17.59 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       19.76         1.71        15.98        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY 
        0.99        12.99        24.85        22.78        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        35.87         0.69        25.15        12.99        45.57 
TCGA-ZS-A9CF 
       79.30 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.33               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            114.35             120.82 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             18.28              19.99 
[1] "0.3 - 114.3 (18.3)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED        37       19         0         14          0
  18Q LOSS WILD-TYPE     134       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                  37                134
  STAGE II                 19                 66
  STAGE III                 0                  3
  STAGE IIIA               14                 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      39  20  16   2
  18Q LOSS WILD-TYPE   143  72  58  10
D74V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               39                143
  T2                  20                 72
  T3                  16                 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    55   1
  18Q LOSS WILD-TYPE 195   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     55    1
  18Q LOSS WILD-TYPE  195    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               55                195
  1                1                  2
[1] 2 2
[1] FALSE
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    59   2
  18Q LOSS WILD-TYPE 202   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     59    2
  18Q LOSS WILD-TYPE  202    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               59                202
  1                2                  2
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    28  49
  18Q LOSS WILD-TYPE  87 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     28   49
  18Q LOSS WILD-TYPE   87  198
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               28                 87
  MALE                 49                198
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    66   4
  18Q LOSS WILD-TYPE 270   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     66    4
  18Q LOSS WILD-TYPE  270    3
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                66                270
  YES                4                  3
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18Q LOSS MUTATED                         2                       73
  18Q LOSS WILD-TYPE                       0                      280
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18Q LOSS MUTATED                                  2
  18Q LOSS WILD-TYPE                                5
D74V9, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       73                280
  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    69   1   0   7
  18Q LOSS WILD-TYPE 249  14   1  14
D74V10, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               69                249
  R1                1                 14
  R2                0                  1
  RX                7                 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    35
  18Q LOSS WILD-TYPE                                1   122
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           3    39
  18Q LOSS WILD-TYPE                        14   138
D74V11, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          35                122
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          39                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"
D74V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     5  68
  18Q LOSS WILD-TYPE   8 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5   68
  18Q LOSS WILD-TYPE    8  264
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  8
  NOT HISPANIC OR LATINO               68                264
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    27  25
  19P LOSS WILD-TYPE 202 104
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                52                306 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                25                104 
$`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        49.84 
TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT 
        2.99         5.03         0.26         4.24         4.24         3.32 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IK TCGA-CC-A7IL 
        9.99         8.94        21.34         9.83         8.61         9.14 
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-DD-AAVV TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A496 
       21.83        82.62        80.71         1.84         0.20         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A3CH TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-RC-A7SK 
       81.73        13.68        25.64        20.78        11.80        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-ZP-A9CV 
       36.10         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        38.40        20.81        22.92 
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        17.10        14.76         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 
       23.38         1.12        69.57        44.42        45.93        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-5264 
       36.66         0.66         2.86         3.19         3.39         3.35 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A7IE 
        9.86         9.96        10.36        11.93        11.41         7.13 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.00        13.12        12.56         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       49.15        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-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-A4NK 
       32.52        90.28        30.97        30.15        26.83        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-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-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       14.20        51.35        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-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.54        40.83        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-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        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-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.17        23.74        18.90        15.72        25.08        26.63 
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-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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        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-EP-A12J 
        0.20        14.04        13.15        13.41        13.35        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-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-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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        22.06        14.70        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        15.78        15.65        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        8.75         2.14        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       22.78        13.55        25.71        23.21        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        79.30        11.21 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.20               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            120.82             114.35 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            18.230             19.775 
[1] "0.2 - 120.8 (18.2)" "0.0 - 114.3 (19.8)"
[1] "hr=" "1.5"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED        24       10         0         12          1
  19P LOSS WILD-TYPE     147       75         3         48          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                147
  STAGE II                 10                 75
  STAGE III                 0                  3
  STAGE IIIA               12                 48
  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  11  13   3
  19P LOSS WILD-TYPE   155  81  61   9
D75V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               27                155
  T2                  11                 81
  T3                  13                 61
  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    39   1
  19P LOSS WILD-TYPE 211   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     39    1
  19P LOSS WILD-TYPE  211    2
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               39                211
  1                1                  2
[1] 2 2
[1] FALSE
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    44   0
  19P LOSS WILD-TYPE 217   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     44    0
  19P LOSS WILD-TYPE  217    4
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               44                217
  1                0                  4
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    12  42
  19P LOSS WILD-TYPE 103 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     12   42
  19P LOSS WILD-TYPE  103  205
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               12                103
  MALE                 42                205
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    47   0
  19P LOSS WILD-TYPE 289   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     47    0
  19P LOSS WILD-TYPE  289    7
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                47                289
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19P LOSS MUTATED                         0                       52
  19P LOSS WILD-TYPE                       2                      301
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19P LOSS MUTATED                                  2
  19P LOSS WILD-TYPE                                5
D75V9, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       52                301
  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    45   4   0   4
  19P LOSS WILD-TYPE 273  11   1  17
D75V10, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               45                273
  R1                4                 11
  R2                0                  1
  RX                4                 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
  19P LOSS MUTATED                                  0    33
  19P LOSS WILD-TYPE                                1   124
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           2    19
  19P LOSS WILD-TYPE                        15   158
D75V11, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          33                124
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          19                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"
D75V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3  50
  19P LOSS WILD-TYPE  10 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3   50
  19P LOSS WILD-TYPE   10  282
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               50                282
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    18  18
  19Q LOSS WILD-TYPE 211 111
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                36                322 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                18                111 
$`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-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF 
        4.24         4.24         3.32         9.99         8.94        21.34 
TCGA-CC-A7IG TCGA-CC-A7IK TCGA-CC-A7IL TCGA-DD-A11A TCGA-DD-A1EI TCGA-DD-A1EJ 
        9.83         8.61         9.14         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        36.10         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        49.84        47.74        18.25        11.74        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       20.81        22.92         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        17.10        14.76         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        23.38         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        45.93        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-5264 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.19         3.39         3.35         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
       11.93        11.41         7.13        12.00        13.12        12.56 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        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-A1EH TCGA-DD-A1EK 
       75.65        11.47        12.95        45.11        49.15        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-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        30.15        26.83        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-AACT TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       13.64        14.20        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-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-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-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        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-AAE9 
       20.98        18.61        19.99         4.64        21.17        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        26.63        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        35.08        79.07        89.69        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       80.71        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        29.92        26.93        28.08        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-A7M5 
       25.25        22.95        20.42        17.10        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89         8.75         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83        11.80         2.14        21.60        31.27 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       29.79        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 
       22.95        24.56        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       26.27        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       19.04        15.39        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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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        35.87         0.69        25.15        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 
              0.26               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            120.82             114.35 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            18.230             19.775 
[1] "0.3 - 120.8 (18.2)" "0.0 - 114.3 (19.8)"
[1] "hr=" "1.5"
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     156       78         3         50          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                156
  STAGE II                  7                 78
  STAGE III                 0                  3
  STAGE IIIA               10                 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
  19Q LOSS MUTATED      17   8  11   2
  19Q LOSS WILD-TYPE   165  84  63  10
D76V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1               17                165
  T2                   8                 84
  T3                  11                 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"
D76V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    28   1
  19Q LOSS WILD-TYPE 222   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     28    1
  19Q LOSS WILD-TYPE  222    2
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               28                222
  1                1                  2
[1] 2 2
[1] FALSE
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    33   0
  19Q LOSS WILD-TYPE 228   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     33    0
  19Q LOSS WILD-TYPE  228    4
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               33                228
  1                0                  4
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     8  30
  19Q LOSS WILD-TYPE 107 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8   30
  19Q LOSS WILD-TYPE  107  217
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                8                107
  MALE                 30                217
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    32   0
  19Q LOSS WILD-TYPE 304   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     32    0
  19Q LOSS WILD-TYPE  304    7
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                32                304
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19Q LOSS MUTATED                         0                       37
  19Q LOSS WILD-TYPE                       2                      316
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19Q LOSS MUTATED                                  1
  19Q LOSS WILD-TYPE                                6
D76V9, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       37                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
  19Q LOSS MUTATED    31   2   0   4
  19Q LOSS WILD-TYPE 287  13   1  17
D76V10, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               31                287
  R1                2                 13
  R2                0                  1
  RX                4                 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
  19Q LOSS MUTATED                                  0    24
  19Q LOSS WILD-TYPE                                1   133
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           2    12
  19Q LOSS WILD-TYPE                        15   165
D76V11, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          24                133
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          12                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"
D76V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2  35
  19Q LOSS WILD-TYPE  11 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   35
  19Q LOSS WILD-TYPE   11  297
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               35                297
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    16   8
  20P LOSS WILD-TYPE 213 121
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                334 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                121 
$`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        14.76         1.12        11.93 
TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A1EK TCGA-DD-A39Y 
       12.56         9.14         6.94        79.73        18.35         5.62 
TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-AACS TCGA-DD-AACX 
       17.59       102.74        73.81        12.26        59.31         5.59 
TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADM TCGA-ED-A8O5 TCGA-ED-A97K TCGA-MR-A8JO 
       44.22        40.54         0.39        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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       47.74        18.25        38.40        20.81        22.92         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        17.10         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        23.38        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        45.93         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-5264 
        4.24         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD 
        3.32         9.86         9.96        10.36        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        8.94         7.13        21.34         9.83        12.00        13.12 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A114 
        8.61         4.60        11.31         9.17         8.15        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       33.04        13.64        21.14        27.19        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 
       25.81         7.66        70.06        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-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
      108.76         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-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-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY 
       14.20        51.35        51.52        50.33        46.82        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 
        5.62         4.50        18.54        21.63        42.58        22.09 
TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.08        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-AADN 
       37.64        35.67        35.05        34.49        20.91        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-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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        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-EP-A12J 
        0.20        14.04        13.15        13.41         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-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-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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       22.06        14.70        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        8.75         2.14        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
        7.53        58.88        26.27        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        36.10 
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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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        35.87         0.69        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.20               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            102.74             120.82 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             12.41              20.32 
[1] "0.2 - 102.7 (12.4)" "0.0 - 120.8 (20.3)"
[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     162       78         2         55          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                162
  STAGE II                  7                 78
  STAGE III                 1                  2
  STAGE IIIA                5                 55
  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   173  85  67  11
D77V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                9                173
  T2                   7                 85
  T3                   7                 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"
D77V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    21   0
  20P LOSS WILD-TYPE 229   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     21    0
  20P LOSS WILD-TYPE  229    3
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               21                229
  1                0                  3
[1] 2 2
[1] FALSE
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    19   1
  20P LOSS WILD-TYPE 242   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     19    1
  20P LOSS WILD-TYPE  242    3
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               19                242
  1                1                  3
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     8  16
  20P LOSS WILD-TYPE 107 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8   16
  20P LOSS WILD-TYPE  107  231
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                8                107
  MALE                 16                231
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    22   1
  20P LOSS WILD-TYPE 314   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     22    1
  20P LOSS WILD-TYPE  314    6
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                22                314
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20P LOSS MUTATED                         1                       22
  20P LOSS WILD-TYPE                       1                      331
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20P LOSS MUTATED                                  1
  20P LOSS WILD-TYPE                                6
D77V9, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       22                331
  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 296  15   1  19
D77V10, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               22                296
  R1                0                 15
  R2                0                  1
  RX                2                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   144
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           1    10
  20P LOSS WILD-TYPE                        16   167
D77V11, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          13                144
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                          10                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"
D77V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  22
  20P LOSS WILD-TYPE  12 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   22
  20P LOSS WILD-TYPE   12  310
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               22                310
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     9   3
  20Q LOSS WILD-TYPE 220 126
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                12                346 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                126 
$`20Q LOSS MUTATED`
TCGA-2Y-A9H6 TCGA-3K-AAZ8 TCGA-5R-AA1D TCGA-CC-A7IJ TCGA-DD-A113 TCGA-DD-A39Y 
       11.74        13.02        14.76        12.56        79.73         5.62 
TCGA-DD-A3A5 TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-AAD5 TCGA-ED-A8O5 TCGA-MR-A8JO 
      102.74        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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       47.74        18.25        38.40        20.81        22.92         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        17.10 
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        23.38         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        45.93         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         4.24         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        4.24         3.35         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
        9.83        12.00        13.12         8.61         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 
       11.31         9.17         6.94         8.15        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       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-A3A6 
       25.81         7.66        70.06        17.59        20.12       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        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-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-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-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-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        42.58        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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        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        29.92        26.93        28.08 
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-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       14.04        13.15        13.41         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-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-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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       22.06        14.70        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        8.75         2.14        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
        7.53        58.88        26.27        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        36.10 
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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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        35.87         0.69        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       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 
            13.185             19.890 
[1] "5.6 - 102.7 (13.2)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1.7"
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     166       82         2         58          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                166
  STAGE II                  3                 82
  STAGE III                 1                  2
  STAGE IIIA                2                 58
  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   177  89  70  12
D78V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                5                177
  T2                   3                 89
  T3                   4                 70
  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 241   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      9    0
  20Q LOSS WILD-TYPE  241    3
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                9                241
  1                0                  3
[1] 2 2
[1] FALSE
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     9   0
  20Q LOSS WILD-TYPE 252   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      9    0
  20Q LOSS WILD-TYPE  252    4
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                9                252
  1                0                  4
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   7
  20Q LOSS WILD-TYPE 110 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    7
  20Q LOSS WILD-TYPE  110  240
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                5                110
  MALE                  7                240
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    11   1
  20Q LOSS WILD-TYPE 325   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     11    1
  20Q LOSS WILD-TYPE  325    6
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                11                325
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20Q LOSS MUTATED                         1                       11
  20Q LOSS WILD-TYPE                       1                      342
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20Q LOSS MUTATED                                  0
  20Q LOSS WILD-TYPE                                7
D78V9, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       11                342
  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 308  15   1  19
D78V10, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               10                308
  R1                0                 15
  R2                0                  1
  RX                2                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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   153
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           1     7
  20Q LOSS WILD-TYPE                        16   170
D78V11, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                153
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           7                170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1  10
  20Q LOSS WILD-TYPE  12 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   10
  20Q LOSS WILD-TYPE   12  322
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               10                322
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    62  44
  21Q LOSS WILD-TYPE 167  85
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               106                252 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                44                 85 
$`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        49.84        18.25         8.55        10.59 
TCGA-5R-AA1C TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A69H TCGA-BD-A3EP 
       17.10        27.52         5.03        44.42        14.60        13.45 
TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A7II 
        3.39         3.35         3.32        10.36         9.99        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A119 TCGA-DD-A11A 
       12.56         8.61         9.17         8.15         7.33         2.60 
TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL 
       90.71        12.95        45.11        49.15        33.04        13.64 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 
       21.14         5.62        25.81         7.66        13.78        30.61 
TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACD 
       32.52        26.83       114.35        13.48         0.53        12.53 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACP 
       63.48        15.42        53.19         0.30        42.81        13.64 
TCGA-DD-AACU TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AAD8 
       51.52        47.67         5.62        21.63        22.09        40.08 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       13.97        40.47        20.91        29.52        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAE8 TCGA-DD-AAEE TCGA-DD-AAEG 
       66.67        18.25        18.61        21.83        26.63        23.64 
TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66Y 
       59.93        80.71        49.48        53.69        29.92         9.73 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-FV-A23B 
        0.20         0.20         0.62         9.96        11.93        60.89 
TCGA-FV-A2QQ TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25Z TCGA-G3-A7M9 
       23.97         0.33        81.73        13.68        21.53         1.84 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5N0 
       11.80        12.23        13.55         0.89         2.14        37.71 
TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75E 
       17.06        11.80         2.14        31.27        12.72        16.67 
TCGA-MR-A8JO TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-WQ-AB4B 
       10.85        19.04        36.10         0.76         7.04        12.99 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D1 
       22.78        13.55        35.77         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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG 
       20.81        22.92         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        14.76         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        23.38 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12        69.57        45.93         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         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        2.86         3.19         4.24         9.86         9.96        11.93 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.41         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 
        9.14         4.60        11.31         6.94        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57        53.33       113.00         0.46        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI 
       79.40        66.31        19.79        75.65        11.47         6.02 
TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A3 
       18.35        27.19        55.69        19.76        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND 
       20.12       102.74       107.11         0.36        33.14        90.28 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       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-AACF TCGA-DD-AACH 
       11.41        75.65        76.41        55.40        12.00         6.41 
TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS 
       69.11         3.52        58.16        61.68        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 
       51.35        50.33        46.82         5.59         4.50        18.54 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADF 
       42.58        44.22        40.54        40.83        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO 
       37.64        35.67        35.05        34.49         0.39        14.89 
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-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA 
       20.98        19.99         4.64        21.17        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       15.72        25.08        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-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       62.47        66.25        65.39        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       13.35        12.82        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-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       22.85        14.40        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       12.03         0.03         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        58.49        14.86        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       22.06        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       15.65         8.75        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
        2.99        20.75        16.83        21.60        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        22.95        24.56        20.71         7.53 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.33        15.39        15.52        17.59        19.76        16.44 
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-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       20.22        24.85        18.28        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        79.30        11.21 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.20               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            114.35             120.82 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             14.83              20.73 
[1] "0.2 - 114.3 (14.8)" "0.0 - 120.8 (20.7)"
[1] "hr=" "1.5"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED        51       23         1         17          2
  21Q LOSS WILD-TYPE     120       62         2         43          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                  51                120
  STAGE II                 23                 62
  STAGE III                 1                  2
  STAGE IIIA               17                 43
  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      56  25  22   4
  21Q LOSS WILD-TYPE   126  67  52   8
D79V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               56                126
  T2                  25                 67
  T3                  22                 52
  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    75   2
  21Q LOSS WILD-TYPE 175   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     75    2
  21Q LOSS WILD-TYPE  175    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               75                175
  1                2                  1
[1] 2 2
[1] FALSE
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    83   3
  21Q LOSS WILD-TYPE 178   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     83    3
  21Q LOSS WILD-TYPE  178    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               83                178
  1                3                  1
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    27  81
  21Q LOSS WILD-TYPE  88 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     27   81
  21Q LOSS WILD-TYPE   88  166
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               27                 88
  MALE                 81                166
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    99   2
  21Q LOSS WILD-TYPE 237   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     99    2
  21Q LOSS WILD-TYPE  237    5
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                99                237
  YES                2                  5
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  21Q LOSS MUTATED                         2                      104
  21Q LOSS WILD-TYPE                       0                      249
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  21Q LOSS MUTATED                                  2
  21Q LOSS WILD-TYPE                                5
D79V9, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                      104                249
  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    94   4   1   5
  21Q LOSS WILD-TYPE 224  11   0  16
D79V10, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               94                224
  R1                4                 11
  R2                1                  0
  RX                5                 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
  21Q LOSS MUTATED                                  0    50
  21Q LOSS WILD-TYPE                                1   107
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           6    48
  21Q LOSS WILD-TYPE                        11   129
D79V11, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          50                107
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          48                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     5  96
  21Q LOSS WILD-TYPE   8 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5   96
  21Q LOSS WILD-TYPE    8  236
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  8
  NOT HISPANIC OR LATINO               96                236
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    38  26
  22Q LOSS WILD-TYPE 191 103
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                64                294 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                26                103 
$`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        49.84        47.74        10.78        14.76 
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A8YO 
       37.32        27.52        45.93         0.26        17.98        18.48 
TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A5UD TCGA-CC-A7IK 
       13.45         2.86         3.35         3.32         9.99         8.61 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A39X 
       11.31         9.17        79.73        37.78         2.60        55.69 
TCGA-DD-A39Y TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO 
        5.62       107.11        32.52        26.83        30.51        73.81 
TCGA-DD-A4NP TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACZ TCGA-DD-AADF TCGA-DD-AADQ 
      108.76         9.30         0.53         5.62         3.78        14.33 
TCGA-DD-AADS TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX 
       15.58        18.61        26.63        29.92         9.73         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T 
       14.04        13.15        19.59        81.73        13.68        51.06 
TCGA-G3-A5SI TCGA-G3-A7M5 TCGA-G3-A7M9 TCGA-G3-AAV3 TCGA-K7-A5RG TCGA-K7-AAU7 
       25.25        14.70         1.84        13.55        17.06        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-QA-A7B7 
       21.60        31.27        22.95        20.71        10.85         3.09 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-WQ-AB4B 
       36.10         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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       20.81        22.92         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        17.10         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        23.38 
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         4.24         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.41         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A9FS TCGA-CC-A9FW 
       13.12        12.56         9.14         4.60         6.94         8.15 
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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        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        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 
       13.91        13.35        12.82         0.20        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-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.33         0.39        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       19.23        22.95        20.42        17.10        22.06        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89         8.75         2.14        11.87        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.20         2.99        37.71        20.75        16.83         2.14 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       29.79        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       24.56         7.53        58.88        26.27        17.69        21.01 
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-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-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
       11.34         0.99        20.22        24.85        18.28        22.78 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        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 
             16.01              20.32 
[1] "0.2 - 120.8 (16.0)" "0.0 - 114.3 (20.3)"
[1] "hr=" "1.2"
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     148       64         3         47          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                148
  STAGE II                 21                 64
  STAGE III                 0                  3
  STAGE IIIA               13                 47
  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   158  67  60   9
D80V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1               24                158
  T2                  25                 67
  T3                  14                 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"
D80V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    43   0
  22Q LOSS WILD-TYPE 207   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     43    0
  22Q LOSS WILD-TYPE  207    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               43                207
  1                0                  3
[1] 2 2
[1] FALSE
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    50   1
  22Q LOSS WILD-TYPE 211   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     50    1
  22Q LOSS WILD-TYPE  211    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               50                211
  1                1                  3
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    24  42
  22Q LOSS WILD-TYPE  91 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     24   42
  22Q LOSS WILD-TYPE   91  205
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               24                 91
  MALE                 42                205
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    60   2
  22Q LOSS WILD-TYPE 276   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     60    2
  22Q LOSS WILD-TYPE  276    5
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                60                276
  YES                2                  5
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  22Q LOSS MUTATED                         2                       62
  22Q LOSS WILD-TYPE                       0                      291
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  22Q LOSS MUTATED                                  2
  22Q LOSS WILD-TYPE                                5
D80V9, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       62                291
  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 266  10   1  13
D80V10, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               52                266
  R1                5                 10
  R2                0                  1
  RX                8                 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
  22Q LOSS MUTATED                                  0    22
  22Q LOSS WILD-TYPE                                1   135
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           8    36
  22Q LOSS WILD-TYPE                         9   141
D80V11, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          22                135
  BLACK OR AFRICAN AMERICAN                       8                  9
  WHITE                                          36                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"
D80V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     5  56
  22Q LOSS WILD-TYPE   8 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5   56
  22Q LOSS WILD-TYPE    8  276
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  8
  NOT HISPANIC OR LATINO               56                276
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    64  27
  XP LOSS WILD-TYPE 165 102
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               91               267 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               27               102 
$`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        17.10         5.03        45.93        17.98        12.72 
TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A3MA TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IG 
        0.66         3.35         9.96         9.99         8.94         9.83 
TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
       12.00         9.14         6.94        37.78        83.57        53.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A39V TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NO 
        2.60         0.46        21.14        33.14        30.97        73.81 
TCGA-DD-A73B TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACS 
        9.30        15.42        53.19        42.81        61.68        59.31 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD8 
       51.52        50.33        46.82        47.67        44.22        40.08 
TCGA-DD-AADC TCGA-DD-AADL TCGA-DD-AADP TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       13.97        20.91        15.06        18.87        19.30        18.25 
TCGA-DD-AAE2 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ 
       20.98        21.83        25.08        25.78        79.07        89.69 
TCGA-DD-AAVU TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A97K 
       72.39        65.39        29.92         0.20         0.20         0.20 
TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U 
       22.85        19.10        27.88         0.33        13.68        53.79 
TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       22.06        14.70        15.65        12.23        13.55         0.89 
TCGA-G3-AAV7 TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MI-A75E 
       11.87        37.71        16.83        31.27        13.97        16.67 
TCGA-MI-A75G TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 
       22.95         3.09        19.33        15.39        15.52         0.76 
TCGA-UB-A7MC TCGA-UB-A7MF TCGA-ZP-A9CV TCGA-ZP-A9D2 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       16.44         7.04        35.77        25.15        40.80        79.30 
TCGA-ZS-A9CG 
       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        49.84        18.25        38.40        20.81        22.92 
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 
       14.76         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        23.38 
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         4.24         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         9.86        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IJ 
       11.93        11.41         7.13        21.34        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 
        8.61         4.60        11.31         9.17         8.15        79.73 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
      113.00         7.33        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-A39W 
       49.15         6.02        33.04        18.35        13.64        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       30.61        32.52        90.28        30.15        26.83        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-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        23.93        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-AACH 
       76.41        55.40        12.53        63.48        12.00         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       69.11         0.30         3.52        58.16        13.64        14.20 
TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       51.35         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE 
       42.58        22.09        40.54        40.83        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
        3.78        37.64        35.67        35.05        34.49         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-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        18.15        18.61        19.99         4.64        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI 
       23.74        18.90        15.72        26.63        23.64        50.33 
TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       35.08        82.62        59.93        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       64.77        62.47        66.25        49.48        53.69        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO 
       28.08        13.91        13.35         9.73        12.82        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41        13.35         1.84        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-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97         8.12         6.38        12.03         0.03 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       81.73         0.39        51.06        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 
       19.23        25.25        22.95        20.42        17.10        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV5 
       11.87        14.14         1.84        15.78        11.80         8.75 
TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF 
        2.14        22.92         1.02         2.20         2.99        20.75 
TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06        11.80         2.14        21.60        29.79        12.72 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        24.56        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF 
       58.88        26.27        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 
       36.10        17.59        19.76         1.71        15.98        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.32        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       18.28        22.78        13.55        25.71        23.21        35.87 
TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
        0.69        12.99        45.57 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.20              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            89.69            120.82 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            19.30             19.79 
[1] "0.2 - 89.7 (19.3)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
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     127       61         3         47          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               127
  STAGE II                24                61
  STAGE III                0                 3
  STAGE IIIA              13                47
  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   136  64  59  10
D81V4, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1              46               136
  T2                 28                64
  T3                 15                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"
D81V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    65   1
  XP LOSS WILD-TYPE 185   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     65    1
  XP LOSS WILD-TYPE  185    2
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              65               185
  1               1                 2
[1] 2 2
[1] FALSE
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    72   1
  XP LOSS WILD-TYPE 189   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     72    1
  XP LOSS WILD-TYPE  189    3
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              72               189
  1               1                 3
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    18  74
  XP LOSS WILD-TYPE  97 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     18   74
  XP LOSS WILD-TYPE   97  173
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              18                97
  MALE                74               173
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    85   3
  XP LOSS WILD-TYPE 251   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     85    3
  XP LOSS WILD-TYPE  251    4
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               85               251
  YES               3                 4
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XP LOSS MUTATED                         0                       89
  XP LOSS WILD-TYPE                       2                      264
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XP LOSS MUTATED                                  3
  XP LOSS WILD-TYPE                                4
D81V9, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      89               264
  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 236  13   1  13
D81V10, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              82               236
  R1               2                13
  R2               0                 1
  RX               8                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
  XP LOSS MUTATED                                  0    46
  XP LOSS WILD-TYPE                                1   111
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                           5    40
  XP LOSS WILD-TYPE                        12   137
D81V11, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         46               111
  BLACK OR AFRICAN AMERICAN                      5                12
  WHITE                                         40               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"
D81V12, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     3  84
  XP LOSS WILD-TYPE  10 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3   84
  XP LOSS WILD-TYPE   10  248
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                10
  NOT HISPANIC OR LATINO              84               248
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    46  22
  XQ LOSS WILD-TYPE 183 107
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               68               290 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               22               107 
$`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-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7IL 
       45.93        17.98         9.96         9.99         9.83         9.14 
TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A4NA 
        6.94        37.78        83.57        53.33         0.46        33.14 
TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO 
       73.81         9.30        15.42        53.19        42.81        61.68 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD8 
       51.52        50.33        46.82        47.67        44.22        40.08 
TCGA-DD-AADC TCGA-DD-AADL TCGA-DD-AADP TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       13.97        20.91        15.06        18.87        19.30        18.25 
TCGA-DD-AAE2 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVU TCGA-ED-A459 
       20.98        21.83        25.08        25.78        72.39        29.92 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A97K TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-G3-A6UC 
        0.20         0.20         0.20        19.10        27.88        22.06 
TCGA-G3-A7M5 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-HP-A5N0 
       14.70        15.65        12.23         0.89        11.87        37.71 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MI-A75E TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SH 
       31.27        13.97        16.67         3.09        19.33        15.39 
TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MF TCGA-ZP-A9CV TCGA-ZP-A9D2 
       15.52         0.76        16.44         7.04        35.77        25.15 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       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        49.84        47.74        18.25 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       38.40        20.81        22.92         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        17.10        14.76         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        23.38         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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
        3.39         4.24         3.35         3.32         9.86        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH 
       11.93        11.41         8.94         7.13        21.34        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       13.12        12.56         8.61         4.60        11.31         9.17 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
        8.15        79.73       113.00         7.33         2.60        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       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-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-A4NB 
      102.74       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-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-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-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ 
       55.40        12.53        63.48        12.00         6.41        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        0.30         3.52        58.16        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       51.35         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE 
       42.58        22.09        40.54        40.83        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
        3.78        37.64        35.67        35.05        34.49         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-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        18.15        18.61        19.99         4.64        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI 
       23.74        18.90        15.72        26.63        23.64        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV 
       35.08        79.07        89.69        82.62        59.93        80.71 
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        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        9.73        12.82        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        1.84        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-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-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-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 
       20.78        11.87        14.14         1.84        15.78        11.80 
TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       13.55         8.75         2.14        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
        2.99        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G 
       21.60        29.79        12.72        12.03         9.57        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       24.56        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA 
       17.69        21.01        21.04        19.04        36.10        17.59 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       19.76         1.71        15.98        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
        0.99        12.99        20.22        24.85        18.28        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 
       13.55        25.71        23.21        35.87         0.69        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       45.57        11.21 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.20              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            83.57            120.82 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            19.20             19.89 
[1] "0.2 - 83.6 (19.2)"  "0.0 - 120.8 (19.9)"
[1] "hr=" "1.1"
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     141       66         3         51          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               141
  STAGE II                19                66
  STAGE III                0                 3
  STAGE IIIA               9                51
  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   150  70  62  11
D82V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1              32               150
  T2                 22                70
  T3                 12                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"
D82V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    46   1
  XQ LOSS WILD-TYPE 204   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     46    1
  XQ LOSS WILD-TYPE  204    2
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              46               204
  1               1                 2
[1] 2 2
[1] FALSE
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    55   0
  XQ LOSS WILD-TYPE 206   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     55    0
  XQ LOSS WILD-TYPE  206    4
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              55               206
  1               0                 4
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    14  54
  XQ LOSS WILD-TYPE 101 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     14   54
  XQ LOSS WILD-TYPE  101  193
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              14               101
  MALE                54               193
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    65   2
  XQ LOSS WILD-TYPE 271   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     65    2
  XQ LOSS WILD-TYPE  271    5
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               65               271
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XQ LOSS MUTATED                         0                       65
  XQ LOSS WILD-TYPE                       2                      288
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XQ LOSS MUTATED                                  3
  XQ LOSS WILD-TYPE                                4
D82V9, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      65               288
  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 255  14   1  17
D82V10, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              63               255
  R1               1                14
  R2               0                 1
  RX               4                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
  XQ LOSS MUTATED                                  0    38
  XQ LOSS WILD-TYPE                                1   119
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           2    27
  XQ LOSS WILD-TYPE                        15   150
D82V11, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         38               119
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         27               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"
D82V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  62
  XQ LOSS WILD-TYPE  11 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   62
  XQ LOSS WILD-TYPE   11  270
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO              62               270
[1] 2 2
[1] FALSE
