[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/22506983/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/22531240/transformed.cor.cli.txt"

nPatients in clinical file=377, in cluster file=370, common to both=370
[1]  82 370
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               62               308 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               62               308 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              226               144 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              226               144 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               43               327 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               43               327 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               40               330 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               40               330 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               35               335 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               35               335 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               38               332 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               38               332 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               27               343 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               27               343 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               363 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               363 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              134               236 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              134               236 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              110               260 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              110               260 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              116               254 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              116               254 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               67               303 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               67               303 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              109               261 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              109               261 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              110               260 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              110               260 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               73               297 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               73               297 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              184               186 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              184               186 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19               351 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19               351 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               19               351 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               19               351 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                58                312 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                58                312 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                36                334 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                36                334 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                18                352 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                18                352 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                20                350 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                20                350 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                40                330 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                40                330 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                47                323 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                47                323 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                23                347 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                23                347 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                348 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                348 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                337 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                337 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                32                338 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                32                338 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                17                353 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                17                353 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                30                340 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                30                340 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                93                277 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                93                277 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                36                334 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                36                334 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                28                342 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                28                342 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                56                314 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                56                314 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                71                299 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                71                299 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               107                263 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               107                263 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               112                258 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               112                258 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                344 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                344 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                48                322 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                48                322 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               41               329 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               41               329 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               60               310 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               60               310 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               78               292 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               78               292 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               350 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               350 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               33               337 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               33               337 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               38               332 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               38               332 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               52               318 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               52               318 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               41               329 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               41               329 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              105               265 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              105               265 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              146               224 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              146               224 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               29               341 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               29               341 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               37               333 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               37               333 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               31               339 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               31               339 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               94               276 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               94               276 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               16               354 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               16               354 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               21               349 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               21               349 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              196               174 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              196               174 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               45               325 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               45               325 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              119               251 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              119               251 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              110               260 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              110               260 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                47                323 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                47                323 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                78                292 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                78                292 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                307 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                307 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                72                298 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                72                298 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                66                304 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                66                304 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                36                334 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                36                334 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               122                248 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               122                248 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               109                261 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               109                261 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                67                303 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                67                303 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               108                262 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               108                262 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               145                225 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               145                225 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               185                185 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               185                185 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                40                330 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                40                330 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                74                296 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                74                296 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                79                291 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                79                291 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                52                318 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                52                318 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                39                331 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                39                331 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                26                344 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                26                344 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                13                357 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                13                357 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               110                260 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               110                260 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                70                300 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                70                300 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               95               275 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               95               275 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               74               296 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               74               296 
[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 370 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	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=218,	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'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 370 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=63, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
183  95  77  12 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
183  95  77  12 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
183  95  77  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
183  95  77  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    39  20
  1P GAIN WILD-TYPE 196 109
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               59               305 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               20               109 
$`1P GAIN MUTATED`
TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-G3-A25W TCGA-G3-A7M9 TCGA-KR-A7K7 
       26.83        21.17        21.83        30.74         1.84        31.27 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-2Y-A9GX TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-5C-AAPD 
        0.76         7.04        80.28        40.41        56.91         0.66 
TCGA-BC-A10Q TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BW-A5NO TCGA-CC-5262 
       37.32        27.52         2.99        44.42         0.66         3.39 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IK TCGA-CC-A8HU 
       11.41         8.94         7.13        21.34         8.61        11.31 
TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A4NJ TCGA-DD-AACB 
       37.78         2.60        45.11         5.62        30.51        76.41 
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-AAVP TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAW0 TCGA-DD-AAW1 
       66.67        90.48        80.71        76.18        66.25        65.39 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-EP-A26S TCGA-EP-A2KB 
       29.92        26.93         0.20        14.04        19.99        19.59 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-GJ-A3OU 
       25.25        22.95        20.78        11.80        13.55        28.90 
TCGA-MI-A75G TCGA-RC-A7SH TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-AA0U 
       22.95        15.39        19.76        16.44        10.75 

$`1P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAEA 
       17.98        36.66         0.36        90.28        18.87        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       23.64         9.96        22.62         8.12         6.38        81.73 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H 
       22.13        22.06        20.75         2.14        12.72        24.56 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       10.32        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H3 
       63.75        41.79        24.89        27.88       120.82        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       13.02        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-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
       23.38         1.12        45.93         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 
       12.72        18.48        44.81        13.45         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.19         4.24         3.35         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
       10.36        11.93         9.99         9.83        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
       12.56         9.14         4.60         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       79.73        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        11.47        12.95        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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78        30.61        33.14        32.52        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        71.80 
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-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       58.16        42.81        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
        4.50        18.54        42.58        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.83        13.97        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       14.33        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-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY 
       89.69        82.62        59.93        72.39        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       62.47        60.99        53.69        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        9.73         0.20        12.82        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK 
        1.84         0.20        18.74        20.61         0.62        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-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M7 
       19.53        19.23        20.42        17.10        14.70        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 
       14.14        15.78        15.65        12.23         0.89        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14        11.87         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK 
        0.49         0.30        21.04        19.33        19.04        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 
       36.10        27.88         1.71        15.98        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
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-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.20              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            90.48            120.82 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            21.63             19.10 
[1] "0.2 - 90.5 (21.6)"  "0.0 - 120.8 (19.1)"
[1] "hr=" "1.1"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P GAIN MUTATED        25       16         0         12          3          2
  1P GAIN WILD-TYPE     148       71         3         50          6          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P GAIN MUTATED          0         0         0
  1P GAIN WILD-TYPE        2         1         2
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 25               148
  STAGE II                16                71
  STAGE III                0                 3
  STAGE IIIA              12                50
  STAGE IIIB               3                 6
  STAGE IIIC               2                 5
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED    26  18  14   4
  1P GAIN WILD-TYPE 157  77  63   8
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              26               157
  T2              18                77
  T3              14                63
  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    41   0
  1P GAIN WILD-TYPE 213   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     41    0
  1P GAIN WILD-TYPE  213    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              41               213
  1               0                 3
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    45   0
  1P GAIN WILD-TYPE 221   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     45    0
  1P GAIN WILD-TYPE  221    4
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              45               221
  1               0                 4
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    13  49
  1P GAIN WILD-TYPE 105 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     13   49
  1P GAIN WILD-TYPE  105  203
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              13               105
  MALE                49               203
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    56   1
  1P GAIN WILD-TYPE 282   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     56    1
  1P GAIN WILD-TYPE  282    8
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               56               282
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1P GAIN MUTATED                         0                       61
  1P GAIN WILD-TYPE                       3                      299
                   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                 3
  HEPATOCELLULAR CARCINOMA                      61               299
  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    51   5   0   4
  1P GAIN WILD-TYPE 273  12   1  17
D1V10, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              51               273
  R1               5                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
  1P GAIN MUTATED                                  1    33
  1P GAIN WILD-TYPE                                1   125
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           3    25
  1P GAIN WILD-TYPE                        14   158
D1V11, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                         33               125
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         25               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"
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  59
  1P GAIN WILD-TYPE  16 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   59
  1P GAIN WILD-TYPE   16  276
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              59               276
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   143  78
  1Q GAIN WILD-TYPE  92  51
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              221               143 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               78                51 
$`1Q GAIN MUTATED`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 
       11.74        38.40         5.03        17.98        36.66         0.36 
TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       26.83        21.17        21.83        23.64         9.96         8.12 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG 
       30.74        22.13         1.84         2.14        31.27        12.72 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GU 
       24.56         0.76         7.04         0.69        40.80        63.75 
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       41.79        80.28       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       20.81        22.92         8.55        13.02        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10W 
        0.66        17.10        37.32        10.13        27.52         2.99 
TCGA-BC-A10Y TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BW-A5NO 
       23.38        44.42        22.36        14.60        12.72         0.66 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC 
        3.19         3.39         3.35         9.96        11.93        11.41 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IK TCGA-CC-A7IL 
        8.94         7.13        21.34         9.83         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
        4.60        11.31         9.17         8.15        79.73        37.78 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         2.60        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK 
       79.40        11.47        12.95        45.11        49.15        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-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       17.59        13.78        30.61        30.97        30.15        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 
       71.80        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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH 
       18.15         4.64        23.74        15.72        25.08        25.78 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       90.48        89.69        82.62        59.93        80.71        76.18 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A459 
       64.77        62.47        66.25        65.39        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       26.93        13.35         9.73        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.15         1.84        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-G3-A25S 
        0.62        23.97        19.10        12.03         0.03        13.68 
TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL 
       58.49        21.53        19.53        19.23        25.25        20.42 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       17.10        20.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ 
       11.64         2.14        11.87        28.90         1.02         2.99 
TCGA-HP-A5N0 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       37.71        27.25        13.97         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       20.71        17.69        21.04        15.39        15.52        36.10 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 
       19.76        16.44         1.71        15.98        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-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        11.21 

$`1Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A110 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAEA 
       83.24         8.61        69.57        90.28        18.87        18.90 
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A6UC TCGA-K7-A5RF TCGA-UB-AA0V 
       22.62         6.38        81.73        22.06        20.75        10.32 
TCGA-XR-A8TG TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H4 
       29.52        23.80        53.39        24.89        27.88        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9HA TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
       18.25         1.18        14.76         1.51        48.99        27.91 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KF 
       46.78        27.52        25.32         1.12        45.93         0.26 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 
       18.48        44.81        13.45         4.24         2.86         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A7IH TCGA-CC-A7II 
        3.32         9.86        10.36         9.99        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A9FS TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A1EB 
       12.56         6.94        83.57        53.33         0.46        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A1 
       19.79        75.65         6.02        33.04        55.69         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB 
       70.06        20.12       102.74       107.11        33.14        32.52 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       56.25       108.76        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACG 
       23.05         1.45        35.67        75.65        12.53        15.42 
TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD6 
        6.41         0.30        50.33        46.82         5.62        22.09 
TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS 
       40.83        39.52         3.78        29.52        14.33        15.58 
TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAEE TCGA-DD-AAEI 
       19.30        20.98        18.61        19.99        26.63        50.33 
TCGA-DD-AAEK TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAW2 TCGA-ED-A5KG TCGA-ED-A627 
       35.08        72.39        56.48        60.99        28.08        13.91 
TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        13.41        13.35         0.20        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
       60.89        27.88         0.33         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A7M5 
       28.27        14.86        25.64         5.92        22.95        14.70 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV4 TCGA-GJ-A9DB TCGA-K7-A5RG 
       11.87        14.14        15.78         0.89         2.20        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-A6M4 TCGA-RC-A6M5 
       58.88        26.27        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-AA0U TCGA-WX-AA46 
        0.30        19.33        19.04        27.88        10.75        24.85 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZS-A9CF 
       33.86        30.41        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             19.99 
[1] "0.0 - 120.8 (19.8)" "0.2 - 108.8 (20.0)"
[1] "hr=" "1"  
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED       103       59         2         31          6          3
  1Q GAIN WILD-TYPE      70       28         1         31          3          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q GAIN MUTATED          2         0         2
  1Q GAIN WILD-TYPE        0         1         0
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                103                70
  STAGE II                59                28
  STAGE III                2                 1
  STAGE IIIA              31                31
  STAGE IIIB               6                 3
  STAGE IIIC               3                 4
  STAGE IV                 2                 0
  STAGE IVA                0                 1
  STAGE IVB                2                 0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q GAIN MUTATED   110  64  42   8
  1Q GAIN WILD-TYPE  73  31  35   4
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1             110                73
  T2              64                31
  T3              42                35
  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   157   0
  1Q GAIN WILD-TYPE  97   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    157    0
  1Q GAIN WILD-TYPE   97    3
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             157                97
  1               0                 3
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   164   4
  1Q GAIN WILD-TYPE 102   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    164    4
  1Q GAIN WILD-TYPE  102    0
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             164               102
  1               4                 0
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    69 157
  1Q GAIN WILD-TYPE  49  95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     69  157
  1Q GAIN WILD-TYPE   49   95
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              69                49
  MALE               157                95
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   209   5
  1Q GAIN WILD-TYPE 129   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    209    5
  1Q GAIN WILD-TYPE  129    4
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              209               129
  YES               5                 4
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1Q GAIN MUTATED                         0                      223
  1Q GAIN WILD-TYPE                       3                      137
                   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                 3
  HEPATOCELLULAR CARCINOMA                     223               137
  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   201   9   1  12
  1Q GAIN WILD-TYPE 123   8   0   9
D2V10, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             201               123
  R1               9                 8
  R2               1                 0
  RX              12                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  2   105
  1Q GAIN WILD-TYPE                                0    53
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          11   102
  1Q GAIN WILD-TYPE                         6    81
D2V11, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                        105                53
  BLACK OR AFRICAN AMERICAN                     11                 6
  WHITE                                        102                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     8 208
  1Q GAIN WILD-TYPE   8 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8  208
  1Q GAIN WILD-TYPE    8  127
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                 8
  NOT HISPANIC OR LATINO             208               127
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    20  21
  2P GAIN WILD-TYPE 215 108
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               41               323 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               21               108 
$`2P GAIN MUTATED`
TCGA-BC-A5W4 TCGA-ES-A2HS TCGA-G3-A25W TCGA-LG-A6GG TCGA-2Y-A9GU TCGA-2Y-A9GY 
       17.98        22.62        30.74        12.72        63.75        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-5R-AA1C TCGA-BC-4072 TCGA-BC-A10Q 
       27.88        56.91        18.25        17.10        48.99        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-CC-A3M9 TCGA-CC-A7IE TCGA-CC-A7IJ TCGA-CC-A7IK 
       10.13        27.52         9.86         7.13        12.56         8.61 
TCGA-DD-A113 TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A9 
       79.73        90.71        45.11        33.04        55.69        30.61 
TCGA-DD-A4NA TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACI 
       33.14        22.78         1.45        13.48        76.41        53.19 
TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADO TCGA-DD-AAVW TCGA-ED-A7PY TCGA-ED-A82E 
        5.62        22.09        14.89        76.18        12.82        13.41 
TCGA-ED-A8O6 TCGA-G3-A25T TCGA-G3-A25Z TCGA-UB-A7MA TCGA-YA-A8S7 
        1.84        51.06        21.53        27.88        13.55 

$`2P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64         9.96         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       81.73        22.13        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       31.27        24.56         0.76         7.04        10.32        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX 
        0.69        40.80        23.80        53.39        41.79        80.28 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
      120.82        40.41        49.84        47.74        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        10.78        10.59         0.66 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       14.76         1.51        27.91        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        14.60        12.72        18.48        44.81        13.45 
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-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-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-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65        11.47        12.95        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-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       13.78        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F 
       80.75        78.84        23.93         9.30        23.05        35.67 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
      114.35         0.53        11.41        75.65        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       71.80        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-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-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        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        60.99        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-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.33         0.39        13.68        53.79        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        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        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
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-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       30.41        22.78        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        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 
            22.78             19.53 
[1] "1.4 - 90.7 (22.8)"  "0.0 - 120.8 (19.5)"
[1] "hr=" "1.4"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P GAIN MUTATED        14       10         0         11          1          2
  2P GAIN WILD-TYPE     159       77         3         51          8          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P GAIN MUTATED          1         0         1
  2P GAIN WILD-TYPE        1         1         1
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 14               159
  STAGE II                10                77
  STAGE III                0                 3
  STAGE IIIA              11                51
  STAGE IIIB               1                 8
  STAGE IIIC               2                 5
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P GAIN MUTATED    15  13  13   2
  2P GAIN WILD-TYPE 168  82  64  10
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              15               168
  T2              13                82
  T3              13                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"
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    29   2
  2P GAIN WILD-TYPE 225   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     29    2
  2P GAIN WILD-TYPE  225    1
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              29               225
  1               2                 1
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    29   2
  2P GAIN WILD-TYPE 237   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     29    2
  2P GAIN WILD-TYPE  237    2
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              29               237
  1               2                 2
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    26  17
  2P GAIN WILD-TYPE  92 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     26   17
  2P GAIN WILD-TYPE   92  235
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              26                92
  MALE                17               235
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    40   0
  2P GAIN WILD-TYPE 298   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     40    0
  2P GAIN WILD-TYPE  298    9
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               40               298
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2P GAIN MUTATED                         0                       41
  2P GAIN WILD-TYPE                       3                      319
                   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                 3
  HEPATOCELLULAR CARCINOMA                      41               319
  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    37   5   0   1
  2P GAIN WILD-TYPE 287  12   1  20
D3V10, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              37               287
  R1               5                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
  2P GAIN MUTATED                                  0    15
  2P GAIN WILD-TYPE                                2   143
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           0    28
  2P GAIN WILD-TYPE                        17   155
D3V11, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         15               143
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                         28               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2  41
  2P GAIN WILD-TYPE  14 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   41
  2P GAIN WILD-TYPE   14  294
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              41               294
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    20  18
  2Q GAIN WILD-TYPE 215 111
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               38               326 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               18               111 
$`2Q GAIN MUTATED`
TCGA-ES-A2HS TCGA-G3-A25W TCGA-LG-A6GG TCGA-2Y-A9GY TCGA-2Y-A9H5 TCGA-5R-AA1C 
       22.62        30.74        12.72        24.89        18.25        17.10 
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-CC-A7IE TCGA-CC-A7IJ TCGA-CC-A7IK 
       48.99        37.32        10.13         7.13        12.56         8.61 
TCGA-DD-A113 TCGA-DD-A1E9 TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A73D 
       79.73        90.71        33.04        55.69        30.61        22.78 
TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AACU TCGA-DD-AACZ 
        1.45        13.48        76.41        53.19        51.52         5.62 
TCGA-DD-AAD6 TCGA-DD-AADO TCGA-DD-AADU TCGA-DD-AAVW TCGA-ED-A7PY TCGA-ED-A82E 
       22.09        14.89        18.21        76.18        12.82        13.41 
TCGA-ED-A8O6 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25Z TCGA-G3-AAV6 TCGA-UB-A7MA 
        1.84        13.68        51.06        21.53         2.14        27.88 
TCGA-XR-A8TE TCGA-YA-A8S7 
       30.41        13.55 

$`2Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        81.73        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
        2.14        31.27        24.56         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU 
       29.52         0.69        40.80        23.80        53.39        63.75 
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       41.79        80.28        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       49.84        47.74        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM 
       13.02        10.78        10.59         0.66        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       14.60        12.72        18.48        44.81        13.45         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-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        9.99         8.94        21.34         9.83        12.00        13.12 
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-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        27.19         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      107.11        13.78        33.14        32.52        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-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       23.05        35.67       114.35         0.53        11.41        75.65 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        59.31        51.35        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-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-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       15.58        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        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        60.99        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-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.33         0.39        53.79        28.27        58.49        14.86 
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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        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-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       11.64        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        15.52        36.10        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TF TCGA-ZP-A9CV 
       20.22        24.85        18.28        33.86        22.78        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-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 
            21.81             19.76 
[1] "1.4 - 90.7 (21.8)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q GAIN MUTATED        13       10         0         11          1          1
  2Q GAIN WILD-TYPE     160       77         3         51          8          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q GAIN MUTATED          1         0         1
  2Q GAIN WILD-TYPE        1         1         1
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 13               160
  STAGE II                10                77
  STAGE III                0                 3
  STAGE IIIA              11                51
  STAGE IIIB               1                 8
  STAGE IIIC               1                 6
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED    14  12  13   1
  2Q GAIN WILD-TYPE 169  83  64  11
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              14               169
  T2              12                83
  T3              13                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"
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    31   1
  2Q GAIN WILD-TYPE 223   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     31    1
  2Q GAIN WILD-TYPE  223    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              31               223
  1               1                 2
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    29   2
  2Q GAIN WILD-TYPE 237   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     29    2
  2Q GAIN WILD-TYPE  237    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              29               237
  1               2                 2
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    23  17
  2Q GAIN WILD-TYPE  95 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     23   17
  2Q GAIN WILD-TYPE   95  235
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              23                95
  MALE                17               235
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    37   0
  2Q GAIN WILD-TYPE 301   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     37    0
  2Q GAIN WILD-TYPE  301    9
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               37               301
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2Q GAIN MUTATED                         0                       38
  2Q GAIN WILD-TYPE                       3                      322
                   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                 3
  HEPATOCELLULAR CARCINOMA                      38               322
  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 289  13   1  20
D4V10, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              35               289
  R1               4                13
  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                                2   142
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           0    24
  2Q GAIN WILD-TYPE                        17   159
D4V11, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         16               142
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                         24               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"
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     3  37
  2Q GAIN WILD-TYPE  13 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   37
  2Q GAIN WILD-TYPE   13  298
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              37               298
[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 215 116
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               33               331 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13               116 
$`3P GAIN MUTATED`
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-2Y-A9GS TCGA-5R-AA1C TCGA-BC-A217 TCGA-BC-A69H 
       22.62         6.38        23.80        17.10        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-AACZ TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR 
        5.62        22.09        40.47        20.91        29.52        66.67 
TCGA-DD-AADU TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEE TCGA-ED-A8O6 TCGA-G3-AAV2 
       18.21         4.64        23.74        26.63         1.84        12.23 
TCGA-MI-A75G TCGA-NI-A8LF TCGA-UB-A7ME 
       22.95        26.27        15.98 

$`3P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU 
       10.32        29.52         0.69        40.80        53.39        63.75 
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       41.79        80.28        24.89        27.88       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       56.91        49.84        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        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-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO 
        1.12        44.42         0.26        22.36        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       44.81        13.45         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-A7IE TCGA-CC-A7IF TCGA-CC-A7IH 
       11.41         9.99         8.94         7.13        21.34        12.00 
TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       13.12         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-A119 
        8.15        79.73        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       18.35        13.64        21.14        27.19        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-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-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
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-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF 
       40.08        40.54        40.83        13.97        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO 
       37.64        35.67        35.05        34.49         0.39        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       15.06        14.33        15.58        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAEB TCGA-DD-AAED 
       18.15        20.98        18.61        19.99        15.72        25.08 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        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        60.99        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-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
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-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       15.65        11.80        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       58.88        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0U 
       36.10        27.88        19.76        16.44         1.71        10.75 
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-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        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 

  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             19.79 
[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     155       79         3         56          9          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P GAIN MUTATED          1         0         0
  3P GAIN WILD-TYPE        1         1         2
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 18               155
  STAGE II                 8                79
  STAGE III                0                 3
  STAGE IIIA               6                56
  STAGE IIIB               0                 9
  STAGE IIIC               1                 6
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P GAIN MUTATED    19  10   6   0
  3P GAIN WILD-TYPE 164  85  71  12
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              19               164
  T2              10                85
  T3               6                71
  T4               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    22   1
  3P GAIN WILD-TYPE 232   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     22    1
  3P GAIN WILD-TYPE  232    2
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              22               232
  1               1                 2
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    26   1
  3P GAIN WILD-TYPE 240   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     26    1
  3P GAIN WILD-TYPE  240    3
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              26               240
  1               1                 3
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     7  28
  3P GAIN WILD-TYPE 111 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      7   28
  3P GAIN WILD-TYPE  111  224
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               7               111
  MALE                28               224
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    32   0
  3P GAIN WILD-TYPE 306   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     32    0
  3P GAIN WILD-TYPE  306    9
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               32               306
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3P GAIN MUTATED                         0                       35
  3P GAIN WILD-TYPE                       3                      325
                   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                 3
  HEPATOCELLULAR CARCINOMA                      35               325
  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 293  17   1  17
D5V10, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              31               293
  R1               0                17
  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                                2   141
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           2    16
  3P GAIN WILD-TYPE                        15   167
D5V11, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         17               141
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         16               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"
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  32
  3P GAIN WILD-TYPE  14 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   32
  3P GAIN WILD-TYPE   14  303
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              32               303
[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 215 113
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               36               328 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16               113 
$`3Q GAIN MUTATED`
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A7M9 TCGA-2Y-A9GS TCGA-5C-AAPD TCGA-5R-AA1C 
       22.62         6.38         1.84        23.80         0.66        17.10 
TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-CC-A7IG 
       10.13        45.93        14.60         0.66         9.86         9.83 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-DD-A114 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EJ 
       12.56         8.61        37.78        21.76        12.95        33.04 
TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-AACL TCGA-DD-AACZ TCGA-DD-AADD 
        5.62        78.84         1.45         3.52         5.62        40.47 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE6 TCGA-DD-AAE9 
       20.91        29.52        66.67        18.21         4.64        23.74 
TCGA-DD-AAEE TCGA-DD-AAVS TCGA-LG-A9QD TCGA-MI-A75G TCGA-NI-A8LF TCGA-UB-A7MD 
       26.63        59.93        12.03        22.95        26.27         1.71 

$`3Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 
       81.73        30.74        22.13        22.06        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       31.27        12.72        24.56         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       29.52         0.69        40.80        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       80.28        24.89        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       49.84        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1D TCGA-5R-AAAM 
        8.55        13.02        10.78        10.59        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-A216 TCGA-BC-A3KF 
        2.99        25.32        23.38         1.12        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 
       22.36        12.72        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-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-A7IL TCGA-CC-A8HT 
        7.13        21.34        12.00        13.12         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 
       11.31         9.17         6.94         8.15        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       53.33       113.00         7.33         2.60         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15         6.02        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        55.69        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       80.75        23.93         9.30        23.05        22.78        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       53.19        69.11         0.30        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       13.97        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
       34.49         0.39        14.89        15.06        14.33        15.58 
TCGA-DD-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-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       19.99        15.72        25.08        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       90.48        89.69        82.62        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        60.99 
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-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-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.39        13.68        51.06        53.79        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-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-A7M5 TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10        14.70        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-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E 
       11.80        27.25        29.79        13.97         9.57        16.67 
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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        36.10        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       16.44        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       12.99        45.57        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             19.99 
[1] "0.7 - 78.8 (15.9)"  "0.0 - 120.8 (20.0)"
[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     154       78         3         57          8          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q GAIN MUTATED          1         0         0
  3Q GAIN WILD-TYPE        1         1         2
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 19               154
  STAGE II                 9                78
  STAGE III                0                 3
  STAGE IIIA               5                57
  STAGE IIIB               1                 8
  STAGE IIIC               1                 6
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q GAIN MUTATED    20  11   7   0
  3Q GAIN WILD-TYPE 163  84  70  12
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              20               163
  T2              11                84
  T3               7                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"
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    24   1
  3Q GAIN WILD-TYPE 230   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     24    1
  3Q GAIN WILD-TYPE  230    2
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              24               230
  1               1                 2
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    27   1
  3Q GAIN WILD-TYPE 239   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     27    1
  3Q GAIN WILD-TYPE  239    3
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              27               239
  1               1                 3
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     8  30
  3Q GAIN WILD-TYPE 110 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8   30
  3Q GAIN WILD-TYPE  110  222
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               8               110
  MALE                30               222
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    35   0
  3Q GAIN WILD-TYPE 303   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     35    0
  3Q GAIN WILD-TYPE  303    9
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               35               303
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3Q GAIN MUTATED                         0                       37
  3Q GAIN WILD-TYPE                       3                      323
                   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                 3
  HEPATOCELLULAR CARCINOMA                      37               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
  3Q GAIN MUTATED    34   0   0   4
  3Q GAIN WILD-TYPE 290  17   1  17
D6V10, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              34               290
  R1               0                17
  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                                2   141
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                           3    18
  3Q GAIN WILD-TYPE                        14   165
D6V11, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         17               141
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         18               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"
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3  34
  3Q GAIN WILD-TYPE  13 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   34
  3Q GAIN WILD-TYPE   13  301
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              34               301
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    21   6
  4P GAIN WILD-TYPE 214 123
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               27               337 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               123 
$`4P GAIN MUTATED`
TCGA-2Y-A9H6 TCGA-G3-A3CG TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-XR-A8TG TCGA-2Y-A9GU 
       11.74        22.13        12.72         0.76        29.52        63.75 
TCGA-2Y-A9H2 TCGA-2Y-A9H8 TCGA-BC-A10R TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB 
       56.91        20.81        10.13         3.19         9.86        10.36 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A1EC TCGA-DD-A1EH 
        9.83        12.00       113.00         2.60        19.79        49.15 
TCGA-DD-A73G TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AADB TCGA-DD-AADO TCGA-DD-AAVS 
      114.35        53.19        58.16        40.83        14.89        59.93 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-WQ-A9G7 
       13.41        13.35         0.99 

$`4P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        38.40         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        81.73        30.74        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-UB-A7MF TCGA-UB-AA0V TCGA-ZP-A9D1 
        2.14        31.27        24.56         7.04        10.32         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       40.80        23.80        53.39        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-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       14.60        12.72        18.48        44.81        13.45         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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       30.61        33.14        32.52        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-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        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN 
       15.42         6.41        69.11         0.30         3.52        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.54        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU 
       50.33        35.08        90.48        89.69        82.62        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        60.99        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-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       14.04        13.15         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.39        13.68        51.06        53.79        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-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-A7M5 TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10        14.70        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-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.75        11.34        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        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 

  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 
            14.89             19.99 
[1] "0.8 - 114.3 (14.9)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.9"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P GAIN MUTATED        11        6         1          5          0          0
  4P GAIN WILD-TYPE     162       81         2         57          9          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P GAIN MUTATED          0         0         0
  4P GAIN WILD-TYPE        2         1         2
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 11               162
  STAGE II                 6                81
  STAGE III                1                 2
  STAGE IIIA               5                57
  STAGE IIIB               0                 9
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED    13   6   8   0
  4P GAIN WILD-TYPE 170  89  69  12
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              13               170
  T2               6                89
  T3               8                69
  T4               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    19   0
  4P GAIN WILD-TYPE 235   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     19    0
  4P GAIN WILD-TYPE  235    3
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              19               235
  1               0                 3
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    22   0
  4P GAIN WILD-TYPE 244   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     22    0
  4P GAIN WILD-TYPE  244    4
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              22               244
  1               0                 4
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    12  15
  4P GAIN WILD-TYPE 106 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     12   15
  4P GAIN WILD-TYPE  106  237
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              12               106
  MALE                15               237
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    24   1
  4P GAIN WILD-TYPE 314   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     24    1
  4P GAIN WILD-TYPE  314    8
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               24               314
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4P GAIN MUTATED                         0                       27
  4P GAIN WILD-TYPE                       3                      333
                   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                 3
  HEPATOCELLULAR CARCINOMA                      27               333
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    24   1   0   2
  4P GAIN WILD-TYPE 300  16   1  19
D7V10, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              24               300
  R1               1                16
  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                                2   146
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1    14
  4P GAIN WILD-TYPE                        16   169
D7V11, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         12               146
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         14               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"
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  26
  4P GAIN WILD-TYPE  15 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   26
  4P GAIN WILD-TYPE   15  309
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              26               309
[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 230 127
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               357 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               127 
$`4Q GAIN MUTATED`
TCGA-G3-A3CG TCGA-CC-5261 TCGA-CC-A7IG TCGA-DD-A1EC TCGA-DD-AACI TCGA-ED-A82E 
       22.13         3.19         9.83        19.79        53.19        13.41 
TCGA-G3-AAUZ 
       15.78 

$`4Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 
        8.12         6.38        81.73        30.74        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        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-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
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-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
       13.45         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-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-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-A1ED TCGA-DD-A1EE 
       51.29        90.71        79.40        66.31        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        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        71.80        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-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        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        60.99        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-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        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-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV1 
       14.70        20.78        11.87        14.14        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        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        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 

  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             19.99 
[1] "3.2 - 53.2 (15.8)"  "0.0 - 120.8 (20.0)"
[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     170       84         3         61          9          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q GAIN MUTATED          0         0         0
  4Q GAIN WILD-TYPE        2         1         2
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  3               170
  STAGE II                 3                84
  STAGE III                0                 3
  STAGE IIIA               1                61
  STAGE IIIB               0                 9
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     3   3   1   0
  4Q GAIN WILD-TYPE 180  92  76  12
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               3               180
  T2               3                92
  T3               1                76
  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 247   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    0
  4Q GAIN WILD-TYPE  247    3
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               7               247
  1               0                 3
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7   0
  4Q GAIN WILD-TYPE 259   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    0
  4Q GAIN WILD-TYPE  259    4
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               7               259
  1               0                 4
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     2   5
  4Q GAIN WILD-TYPE 116 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    5
  4Q GAIN WILD-TYPE  116  247
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2               116
  MALE                 5               247
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7   0
  4Q GAIN WILD-TYPE 331   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    0
  4Q GAIN WILD-TYPE  331    9
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                7               331
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4Q GAIN MUTATED                         0                        7
  4Q GAIN WILD-TYPE                       3                      353
                   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                 3
  HEPATOCELLULAR CARCINOMA                       7               353
  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 319  16   1  20
D8V10, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               5               319
  R1               1                16
  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                                2   154
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     2
  4Q GAIN WILD-TYPE                        17   181
D8V11, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4               154
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                          2               181
[1] 4 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  15 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    6
  4Q GAIN WILD-TYPE   15  329
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO               6               329
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    73  59
  5P GAIN WILD-TYPE 162  70
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              132               232 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               59                70 
$`5P GAIN MUTATED`
TCGA-BC-A112 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL 
        5.03         0.36        90.28        18.90        23.64         9.96 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-LG-A6GG TCGA-UB-A7MF TCGA-ZP-A9D1 
       81.73        30.74        22.13        12.72         7.04         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       40.80        41.79        24.89        27.88        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       49.84        47.74        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A217 
       13.02        10.78        37.32        10.13         2.99        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-A4NK TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       39.78        73.81        78.84       114.35        13.48         0.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACV 
       12.00        15.42        53.19        69.11        13.64        50.33 
TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADF 
        5.62        21.63        44.22        40.08        13.97         3.78 
TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE3 
       29.52        14.33        66.67        18.21        18.25        18.61 
TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVV TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW2 
       26.63        35.08        80.71        64.77        66.25        60.99 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       29.92        13.35         9.73        14.04        13.15        13.41 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 
        1.84        19.59         0.62        14.40        19.10        27.88 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SI TCGA-G3-A5SM 
        0.03         0.39        51.06        58.49        25.25        17.10 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       14.70        11.80        12.23        11.64         2.20         2.99 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
       27.25        29.79        13.97        22.95        20.71        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-AA0U 
       17.69        21.01        19.04        36.10        15.98        10.75 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CZ TCGA-ZP-A9D2 
        0.99        12.99        18.28        22.78        23.21        25.15 

$`5P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-ES-A2HS 
       36.66        26.83        18.87        21.17        21.83        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
        8.12         6.38        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TG TCGA-2Y-A9GS 
       31.27        24.56         0.76        10.32        29.52        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H5 TCGA-5C-A9VH 
       53.39        63.75        80.28       120.82        18.25        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-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52        27.52        25.32        23.38         1.12 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       44.42         0.26        14.60        12.72        18.48        44.81 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 
        0.66         4.24         2.86         3.19         3.39         9.86 
TCGA-CC-A3MA TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IJ 
        9.96         8.94         7.13        21.34        12.00        12.56 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 
        8.61         4.60         9.17         6.94        79.73        37.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EC TCGA-DD-A1ED 
        7.33         2.60         0.46        21.76        19.79        75.65 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        33.04        18.35        13.64 
TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 
       27.19        19.76        25.81        70.06        20.12       107.11 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       30.61        33.14        32.52        30.97        30.15        30.51 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56       108.76        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.35        51.52        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA 
       47.67         4.50        18.54        42.58        22.09        40.54 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.83        40.47        39.52        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADS 
       34.49        20.91         0.39        14.89        15.06        15.58 
TCGA-DD-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-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        90.48 
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-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3R3 
       19.99        20.61        11.93        60.89        23.97        12.03 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
        0.33        13.68        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       25.64         5.92        19.53        19.23        22.95        20.42 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV3 
       20.78        11.87        14.14        15.78        15.65        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5N0 
        0.89         2.14        11.87        28.90         1.02        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       17.06        16.83        11.80        12.03         9.57        16.67 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
        7.53        10.85        26.27         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA 
        0.30        21.04        19.33        15.39        15.52        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 
       19.76        16.44         1.71        11.34        20.22        24.85 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
       33.86        30.41        13.55        35.77        25.71        35.87 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        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 
           18.445            20.320 
[1] "0.0 - 114.3 (18.4)" "0.2 - 120.8 (20.3)"
[1] "hr=" "1.4"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P GAIN MUTATED        55       33         1         29          4          1
  5P GAIN WILD-TYPE     118       54         2         33          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P GAIN MUTATED          1         0         0
  5P GAIN WILD-TYPE        1         1         2
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 55               118
  STAGE II                33                54
  STAGE III                1                 2
  STAGE IIIA              29                33
  STAGE IIIB               4                 5
  STAGE IIIC               1                 6
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P GAIN MUTATED    58  37  36   3
  5P GAIN WILD-TYPE 125  58  41   9
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              58               125
  T2              37                58
  T3              36                41
  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 165   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     89    0
  5P GAIN WILD-TYPE  165    3
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              89               165
  1               0                 3
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    96   1
  5P GAIN WILD-TYPE 170   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     96    1
  5P GAIN WILD-TYPE  170    3
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              96               170
  1               1                 3
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    41  93
  5P GAIN WILD-TYPE  77 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     41   93
  5P GAIN WILD-TYPE   77  159
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              41                77
  MALE                93               159
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   123   5
  5P GAIN WILD-TYPE 215   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    123    5
  5P GAIN WILD-TYPE  215    4
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO              123               215
  YES               5                 4
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5P GAIN MUTATED                         0                      131
  5P GAIN WILD-TYPE                       3                      229
                   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                 3
  HEPATOCELLULAR CARCINOMA                     131               229
  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   119   6   0   6
  5P GAIN WILD-TYPE 205  11   1  15
D9V10, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0             119               205
  R1               6                11
  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                                2   100
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           7    62
  5P GAIN WILD-TYPE                        10   121
D9V11, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         58               100
  BLACK OR AFRICAN AMERICAN                      7                10
  WHITE                                         62               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"
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     5 121
  5P GAIN WILD-TYPE  11 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5  121
  5P GAIN WILD-TYPE   11  214
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                11
  NOT HISPANIC OR LATINO             121               214
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    60  48
  5Q GAIN WILD-TYPE 175  81
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              108               256 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               48                81 
$`5Q GAIN MUTATED`
TCGA-BC-A112 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL 
        5.03         0.36        90.28        18.90        23.64         9.96 
TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-LG-A6GG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        6.38        30.74        22.13        12.72         0.69        40.80 
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-CC-5264 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A7IG 
        2.99         3.35        10.36        11.93        11.41         9.83 
TCGA-CC-A7IL TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11D 
        9.14         8.15        83.57        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-A4NK TCGA-DD-A4NO 
        7.66        17.59       102.74        13.78        39.78        73.81 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACC 
       78.84        23.93       114.35        13.48         0.53        55.40 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACV 
       12.00        15.42        53.19        69.11        13.64        50.33 
TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AADN 
        5.62        21.63        13.97         3.78         0.39        29.52 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAEK 
       14.33        66.67        18.21        18.25        18.61        35.08 
TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-ED-A459 
       80.71        56.48        64.77        66.25        60.99        29.92 
TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HT 
        9.73        14.04        13.15        19.59         0.62        14.40 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SM TCGA-G3-A7M5 
        0.03         0.39        13.68        51.06        17.10        14.70 
TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-LG-A9QC 
       11.80        11.64         2.20         2.99        27.25        13.97 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF TCGA-RG-A7D4 
       22.95        20.71        26.27        17.69        19.04        36.10 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CZ TCGA-ZP-A9D2 
        0.99        12.99        18.28        22.78        23.21        25.15 

$`5Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-ES-A2HS 
       36.66        26.83        18.87        21.17        21.83        22.62 
TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
        8.12        81.73        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       31.27        24.56         0.76         7.04        10.32        29.52 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H2 
       23.80        53.39        63.75        80.28       120.82        56.91 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       18.25        20.81        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-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
       27.52        25.32        23.38         1.12        44.42        45.93 
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-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45         0.66         4.24         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UD TCGA-CC-A5UE 
        4.24         3.32         9.86         9.96         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-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 
        4.60        11.31         9.17         6.94        79.73        37.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC 
        7.33         2.60         0.46        21.76        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        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-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.15        30.51        56.25        29.56       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
        0.30        80.75         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE 
       35.67        11.41        75.65        76.41        12.53        71.80 
TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.35        51.52        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
       47.67         4.50        18.54        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG 
       40.08        40.54        40.83        40.47        39.52        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP 
       35.67        35.05        34.49        20.91        14.89        15.06 
TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       15.58        19.30        18.25        18.15        20.98        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        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        90.48        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-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       11.93        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        0.33        53.79        28.27        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-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.42        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       12.23        13.55         0.89         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 
        1.02        37.71        17.06        16.83        11.80        29.79 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       12.03         9.57        16.67         7.53        10.85        58.88 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        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        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 
        1.71        15.98        10.75        11.34        20.22        24.85 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
       33.86        30.41        13.55        35.77        25.71        35.87 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.20 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           114.35            120.82 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           18.445            20.170 
[1] "0.0 - 114.3 (18.4)" "0.2 - 120.8 (20.2)"
[1] "hr=" "1.3"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q GAIN MUTATED        49       29         1         18          3          1
  5Q GAIN WILD-TYPE     124       58         2         44          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q GAIN MUTATED          1         0         0
  5Q GAIN WILD-TYPE        1         1         2
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 49               124
  STAGE II                29                58
  STAGE III                1                 2
  STAGE IIIA              18                44
  STAGE IIIB               3                 6
  STAGE IIIC               1                 6
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED    51  33  24   2
  5Q GAIN WILD-TYPE 132  62  53  10
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              51               132
  T2              33                62
  T3              24                53
  T4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    72   0
  5Q GAIN WILD-TYPE 182   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     72    0
  5Q GAIN WILD-TYPE  182    3
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              72               182
  1               0                 3
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    77   1
  5Q GAIN WILD-TYPE 189   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     77    1
  5Q GAIN WILD-TYPE  189    3
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              77               189
  1               1                 3
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    27  83
  5Q GAIN WILD-TYPE  91 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     27   83
  5Q GAIN WILD-TYPE   91  169
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              27                91
  MALE                83               169
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    99   6
  5Q GAIN WILD-TYPE 239   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     99    6
  5Q GAIN WILD-TYPE  239    3
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               99               239
  YES               6                 3
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5Q GAIN MUTATED                         0                      108
  5Q GAIN WILD-TYPE                       3                      252
                   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                 3
  HEPATOCELLULAR CARCINOMA                     108               252
  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   100   5   0   4
  5Q GAIN WILD-TYPE 224  12   1  17
D10V10, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0             100               224
  R1               5                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
  5Q GAIN MUTATED                                  0    47
  5Q GAIN WILD-TYPE                                2   111
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           6    52
  5Q GAIN WILD-TYPE                        11   131
D10V11, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         47               111
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         52               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     5 100
  5Q GAIN WILD-TYPE  11 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5  100
  5Q GAIN WILD-TYPE   11  235
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                11
  NOT HISPANIC OR LATINO             100               235
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    70  42
  6P GAIN WILD-TYPE 165  87
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              112               252 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               42                87 
$`6P GAIN MUTATED`
TCGA-4R-AA8I TCGA-DD-A3A8 TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A3CG TCGA-G3-A6UC 
        8.61         0.36        22.62         6.38        22.13        22.06 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       12.72        24.56         7.04        23.80        24.89        27.88 
TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG 
       49.84        18.25        20.81         1.18        13.02        10.78 
TCGA-5R-AA1C TCGA-BC-A10U TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BD-A2L6 
       17.10        27.52        45.93        22.36        14.60        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3MC TCGA-CC-A5UE 
       13.45         0.66         4.24         3.35        11.93         8.94 
TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL 
        7.13         9.83        12.00        13.12         8.61         9.14 
TCGA-CC-A8HU TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39Y 
       11.31        37.78         7.33        45.11        49.15         5.62 
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        71.80        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-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVR 
       18.25        18.61        23.74        25.78        35.08        82.62 
TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 
       59.93        80.71        76.18        64.77        60.99        53.69 
TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB 
       13.35         0.20        13.41        13.35         1.84        19.59 
TCGA-EP-A2KC TCGA-FV-A3I0 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A3CK 
        0.62        27.88        13.68        53.79        58.49        19.23 
TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-KR-A7K2 
       25.25        20.42        11.80        13.55         0.89        27.25 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 
       22.95        20.71        26.27        21.04        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-XR-A8TD 
       27.88        16.44        10.75         0.99        20.22        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD 
       30.41        22.78        13.55        45.57 

$`6P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66        90.28        26.83        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W 
       18.90        23.64         9.96         8.12        81.73        30.74 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-AA0V 
        1.84        20.75         2.14        31.27         0.76        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       29.52         0.69        40.80        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H9 
       80.28       120.82        40.41        56.91        47.74        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-A216 TCGA-BC-A3KF TCGA-BC-A69I 
       25.32        23.38         1.12        44.42         0.26        12.72 
TCGA-BC-A8YO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
       18.48         4.24         2.86         3.19         3.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF 
        9.86         9.96        10.36        11.41         9.99        21.34 
TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
       12.56         4.60         9.17         6.94         8.15        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       11.47        12.95         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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV 
       56.25        73.81       108.76        12.26         0.30        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 
       23.93        23.05        35.67       114.35        13.48        11.41 
TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       55.40        15.42         6.41         0.30         3.52        58.16 
TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       61.68        14.20        59.31        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       44.22        22.09        40.08        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
       39.52         3.78        35.67        35.05        34.49         0.39 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       15.06        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAEB TCGA-DD-AAED 
       18.15        20.98        19.99         4.64        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVX 
       26.63        50.33        90.48        89.69        72.39        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-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91         9.73         0.20        12.82        14.04        13.15 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        18.74        19.99        20.61        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       60.89        23.97        19.10        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
        0.39        51.06        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
        5.92        19.53        22.95        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV5 
       11.87        14.14        15.78        15.65        12.23        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        17.06        16.83        11.80        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       12.03         9.57        16.67         7.53        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       19.33        19.04        15.39        19.76         1.71        15.98 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34        12.99        24.85        18.28        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF TCGA-ZS-A9CG 
       23.21        35.87        25.15        12.99        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 
            20.76             19.43 
[1] "0.2 - 82.6 (20.8)"  "0.0 - 120.8 (19.4)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P GAIN MUTATED        46       32         1         22          4          1
  6P GAIN WILD-TYPE     127       55         2         40          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P GAIN MUTATED          2         0         1
  6P GAIN WILD-TYPE        0         1         1
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 46               127
  STAGE II                32                55
  STAGE III                1                 2
  STAGE IIIA              22                40
  STAGE IIIB               4                 5
  STAGE IIIC               1                 6
  STAGE IV                 2                 0
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P GAIN MUTATED    47  37  28   3
  6P GAIN WILD-TYPE 136  58  49   9
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              47               136
  T2              37                58
  T3              28                49
  T4               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    81   0
  6P GAIN WILD-TYPE 173   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     81    0
  6P GAIN WILD-TYPE  173    3
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              81               173
  1               0                 3
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    83   3
  6P GAIN WILD-TYPE 183   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     83    3
  6P GAIN WILD-TYPE  183    1
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              83               183
  1               3                 1
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    33  83
  6P GAIN WILD-TYPE  85 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     33   83
  6P GAIN WILD-TYPE   85  169
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              33                85
  MALE                83               169
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   109   1
  6P GAIN WILD-TYPE 229   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    109    1
  6P GAIN WILD-TYPE  229    8
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO              109               229
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6P GAIN MUTATED                         0                      113
  6P GAIN WILD-TYPE                       3                      247
                   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                 3
  HEPATOCELLULAR CARCINOMA                     113               247
  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   103   5   1   7
  6P GAIN WILD-TYPE 221  12   0  14
D11V10, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0             103               221
  R1               5                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
  6P GAIN MUTATED                                  1    56
  6P GAIN WILD-TYPE                                1   102
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           7    52
  6P GAIN WILD-TYPE                        10   131
D11V11, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                         56               102
  BLACK OR AFRICAN AMERICAN                      7                10
  WHITE                                         52               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     9 103
  6P GAIN WILD-TYPE   7 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9  103
  6P GAIN WILD-TYPE    7  232
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                 7
  NOT HISPANIC OR LATINO             103               232
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    41  22
  6Q GAIN WILD-TYPE 194 107
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               63               301 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               22               107 
$`6Q GAIN MUTATED`
TCGA-G3-A3CG TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF TCGA-2Y-A9GS TCGA-2Y-A9GY 
       22.13        12.72        24.56         7.04        23.80        24.89 
TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A3KG 
       49.84        18.25         1.18        13.02        10.78        22.36 
TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3MC 
       14.60        44.81        13.45         4.24         3.35        11.93 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-DD-A114 
        8.94         7.13        12.00        13.12         8.61        37.78 
TCGA-DD-A119 TCGA-DD-A1EH TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A73B TCGA-DD-A73D 
        7.33        49.15         5.62        30.61         9.30        22.78 
TCGA-DD-A73E TCGA-DD-AACB TCGA-DD-AACJ TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AADN 
        1.45        76.41        69.11        42.81        51.35        29.52 
TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAEH TCGA-DD-AAEK 
       14.89        14.33        18.25        18.61        25.78        35.08 
TCGA-DD-AAVV TCGA-DD-AAW2 TCGA-ED-A66X TCGA-EP-A2KB TCGA-EP-A2KC TCGA-G3-A25S 
       80.71        60.99        13.35        19.59         0.62        13.68 
TCGA-G3-A25U TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-MI-A75G 
       53.79        19.23        25.25        11.80        27.25        22.95 
TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WX-AA44 TCGA-XR-A8TD 
       21.04        15.52        36.10        16.44        20.22        33.86 
TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZS-A9CD 
       30.41        13.55        45.57 

$`6Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 
        8.12         6.38        81.73        30.74        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TG 
       20.75         2.14        31.27         0.76        10.32        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
        0.69        40.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H8 
       27.88       120.82        40.41        56.91        47.74        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       22.92         8.55        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69I TCGA-BC-A8YO TCGA-BW-A5NO 
       44.42        45.93         0.26        12.72        18.48         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-A1EG TCGA-DD-A1EI 
       19.79        75.65        11.47        12.95        45.11         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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        13.78        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       23.05        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       75.65        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO 
        6.41        53.19         0.30         3.52        58.16        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        59.31        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADR 
       35.05        34.49        20.91         0.39        15.06        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
       15.58        18.21        19.30        18.25        18.15        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        90.48        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-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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V 
       12.03         0.03         0.33         0.39        51.06        28.27 
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-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14        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 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 
        2.99        37.71        17.06        16.83        11.80        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.72         0.49         0.30        19.33        19.04        15.39 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       27.88        19.76         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV 
        0.99        12.99        24.85        18.28        22.78        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       25.71        23.21        35.87        25.15        12.99        79.30 
TCGA-ZS-A9CG 
       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 
            19.23             19.99 
[1] "0.6 - 80.7 (19.2)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q GAIN MUTATED        24       18         1         14          3          1
  6Q GAIN WILD-TYPE     149       69         2         48          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q GAIN MUTATED          2         0         1
  6Q GAIN WILD-TYPE        0         1         1
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 24               149
  STAGE II                18                69
  STAGE III                1                 2
  STAGE IIIA              14                48
  STAGE IIIB               3                 6
  STAGE IIIC               1                 6
  STAGE IV                 2                 0
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED    24  21  18   3
  6Q GAIN WILD-TYPE 159  74  59   9
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              24               159
  T2              21                74
  T3              18                59
  T4               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    48   0
  6Q GAIN WILD-TYPE 206   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     48    0
  6Q GAIN WILD-TYPE  206    3
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              48               206
  1               0                 3
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    45   3
  6Q GAIN WILD-TYPE 221   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     45    3
  6Q GAIN WILD-TYPE  221    1
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              45               221
  1               3                 1
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    18  49
  6Q GAIN WILD-TYPE 100 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     18   49
  6Q GAIN WILD-TYPE  100  203
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              18               100
  MALE                49               203
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    61   1
  6Q GAIN WILD-TYPE 277   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     61    1
  6Q GAIN WILD-TYPE  277    8
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               61               277
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6Q GAIN MUTATED                         0                       66
  6Q GAIN WILD-TYPE                       3                      294
                   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                 3
  HEPATOCELLULAR CARCINOMA                      66               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
  6Q GAIN MUTATED    58   2   1   6
  6Q GAIN WILD-TYPE 266  15   0  15
D12V10, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              58               266
  R1               2                15
  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
  6Q GAIN MUTATED                                  1    31
  6Q GAIN WILD-TYPE                                1   127
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           5    30
  6Q GAIN WILD-TYPE                        12   153
D12V11, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                         31               127
  BLACK OR AFRICAN AMERICAN                      5                12
  WHITE                                         30               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"
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     8  56
  6Q GAIN WILD-TYPE   8 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      8   56
  6Q GAIN WILD-TYPE    8  279
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                 8
  NOT HISPANIC OR LATINO              56               279
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    66  39
  7P GAIN WILD-TYPE 169  90
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              105               259 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               39                90 
$`7P GAIN MUTATED`
TCGA-4R-AA8I TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAEA TCGA-EP-A3JL TCGA-ES-A2HS 
        8.61        90.28        26.83        18.90         9.96        22.62 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A3CG TCGA-LG-A6GG TCGA-ZP-A9D1 TCGA-2Y-A9GS 
        6.38        81.73        22.13        12.72         0.69        23.80 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H8 
       63.75        41.79        24.89        27.88        56.91        20.81 
TCGA-2Y-A9H9 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R 
       22.92        13.02        10.78        10.59        37.32        10.13 
TCGA-BC-A10U TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A3MB 
       27.52        13.45         0.66         2.86         3.35        10.36 
TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A113 
        8.94        13.12        12.56        11.31         8.15        79.73 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE 
      113.00         2.60        51.29        90.71        19.79        11.47 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A7 
       33.04        21.14         5.62        19.76        70.06        13.78 
TCGA-DD-A4NA TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73E 
       33.14        39.78        12.26        78.84        22.78         1.45 
TCGA-DD-A73G TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACP 
      114.35        12.53        71.80        12.00        53.19        13.64 
TCGA-DD-AACT TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AADD TCGA-DD-AADL 
       51.35         5.62         4.50        42.58        40.47        20.91 
TCGA-DD-AADS TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       15.58        18.25        18.61         4.64        23.74        15.72 
TCGA-DD-AAVP TCGA-DD-AAVV TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66Y 
       90.48        80.71        64.77        60.99        53.69         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A496 
        0.20        12.82        14.04         1.84         0.62         0.33 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A5SM 
       13.68        51.06        58.49        19.53        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-MI-A75G 
       14.70        11.80        11.64         2.14        27.25        22.95 
TCGA-NI-A8LF TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       26.27        15.98        10.75         0.99        12.99        24.85 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       30.41        22.78        13.55 

$`7P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEG 
       36.66         0.36        18.87        21.17        21.83        23.64 
TCGA-FV-A3I1 TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
        8.12        30.74        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       31.27        24.56         0.76         7.04        10.32        29.52 
TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 
       40.80        53.39        80.28       120.82        40.41        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-AAPD TCGA-5R-AA1C 
       47.74        18.25         1.18         8.55         0.66        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T 
       14.76         1.51        48.99        27.91        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
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-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-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-A73C TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        9.30        23.05        35.67        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ 
       75.65        76.41        55.40        15.42         6.41        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ 
        0.30         3.52        58.16        42.81        61.68        14.20 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       59.31        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-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-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.83        13.97        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 
       14.33        66.67        18.21        19.30        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       20.98        19.99        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       35.08        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A4XI 
       56.48        62.47        66.25        65.39        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       28.08        13.91        13.35         0.20        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.35         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
       12.03         0.03         0.39        53.79        28.27        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-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-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       13.55         0.89        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 
        2.99        37.71        17.06        16.83        11.80        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-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       10.85        58.88        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34        20.22        18.28        33.86        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 

  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 
            18.61             20.22 
[1] "0.2 - 114.3 (18.6)" "0.0 - 120.8 (20.2)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED        47       27         0         20          3          4
  7P GAIN WILD-TYPE     126       60         3         42          6          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P GAIN MUTATED          1         0         0
  7P GAIN WILD-TYPE        1         1         2
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 47               126
  STAGE II                27                60
  STAGE III                0                 3
  STAGE IIIA              20                42
  STAGE IIIB               3                 6
  STAGE IIIC               4                 3
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P GAIN MUTATED    50  32  24   3
  7P GAIN WILD-TYPE 133  63  53   9
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              50               133
  T2              32                63
  T3              24                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"
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    70   2
  7P GAIN WILD-TYPE 184   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     70    2
  7P GAIN WILD-TYPE  184    1
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              70               184
  1               2                 1
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    79   1
  7P GAIN WILD-TYPE 187   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     79    1
  7P GAIN WILD-TYPE  187    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              79               187
  1               1                 3
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    39  70
  7P GAIN WILD-TYPE  79 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     39   70
  7P GAIN WILD-TYPE   79  182
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              39                79
  MALE                70               182
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   100   2
  7P GAIN WILD-TYPE 238   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    100    2
  7P GAIN WILD-TYPE  238    7
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              100               238
  YES               2                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7P GAIN MUTATED                         0                      108
  7P GAIN WILD-TYPE                       3                      252
                   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                 3
  HEPATOCELLULAR CARCINOMA                     108               252
  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 228  11   1  15
D13V10, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              96               228
  R1               6                11
  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                                  2    42
  7P GAIN WILD-TYPE                                0   116
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           5    58
  7P GAIN WILD-TYPE                        12   125
D13V11, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                         42               116
  BLACK OR AFRICAN AMERICAN                      5                12
  WHITE                                         58               125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     6  99
  7P GAIN WILD-TYPE  10 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6   99
  7P GAIN WILD-TYPE   10  236
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                10
  NOT HISPANIC OR LATINO              99               236
[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 170  88
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              106               258 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               41                88 
$`7Q GAIN MUTATED`
TCGA-4R-AA8I TCGA-BC-A5W4 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAEA TCGA-EP-A3JL 
        8.61        17.98        90.28        26.83        18.90         9.96 
TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A3CG TCGA-G3-A6UC TCGA-LG-A6GG 
       22.62         8.12         6.38        22.13        22.06        12.72 
TCGA-ZP-A9D1 TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ 
        0.69        23.80        63.75        41.79        24.89        27.88 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       56.91        49.84        20.81        22.92        13.02        10.78 
TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BD-A3EP TCGA-BW-A5NO 
       10.59        37.32        10.13        27.52        13.45         0.66 
TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A5UE TCGA-CC-A7II 
        2.86         3.35         9.86        10.36         8.94        13.12 
TCGA-CC-A7IJ TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D 
       12.56        11.31         8.15       113.00         2.60        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39Y 
       90.71        19.79        11.47        33.04        21.14         5.62 
TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A4NA TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-DD-A4NV 
       19.76        70.06        33.14        39.78        12.26        78.84 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE 
       23.05         1.45       114.35        75.65        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AADD TCGA-DD-AADG 
       12.00        53.19        13.64        51.35        40.47        37.64 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADS TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 
       20.91         0.39        15.58        18.61         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAEI TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAW2 TCGA-DD-AAW3 
       15.72        50.33        80.71        56.48        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       29.92         9.73        12.82        19.99        20.61         0.62 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       51.06        58.49        19.53        20.42        17.10        14.70 
TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-MI-A75G TCGA-NI-A4U2 
       11.80        11.64         2.14        27.25        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-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        30.41        22.78        13.55 

$`7Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BD-A3ER 
       83.24        11.74        38.40        69.57         5.03        36.66 
TCGA-DD-A3A8 TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-FV-A4ZP 
        0.36        18.87        21.17        21.83        23.64        81.73 
TCGA-G3-A25W TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H 
       30.74         1.84        20.75         2.14        31.27        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GT 
        0.76         7.04        10.32        29.52        40.80        53.39 
TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9HA 
       80.28       120.82        40.41        47.74        18.25         1.18 
TCGA-2Y-A9HB TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55         0.66        17.10        14.76         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        46.78        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       12.72        18.48        44.81         4.24         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        4.24         3.32         9.96        11.93        11.41         9.99 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL 
        7.13        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-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33         7.33         0.46        21.76        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65        12.95        45.11        49.15         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 
       13.64        27.19        55.69        25.81         7.66        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        30.61        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.97        30.15        30.51        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D 
      108.76         0.30        80.75        23.93         9.30        22.78 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC 
       35.67        13.48         0.53        11.41        76.41        55.40 
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-AACN TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
       42.81        61.68        14.20        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       40.83        13.97        39.52         3.78        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       34.49        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE4 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
       19.99        25.08        26.63        25.78        35.08        90.48 
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-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33         0.39        13.68        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53        25.64         5.92        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       22.95        20.78        11.87        14.14        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        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       29.79        13.97        12.03         9.57        16.67        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
        7.53        10.85        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.49         0.30        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-WJ-A86L 
       36.10        27.88        19.76        16.44        15.98        11.34 
TCGA-WX-AA44 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       20.22        18.28        33.86        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        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            19.460 
[1] "0.4 - 114.3 (20.2)" "0.0 - 120.8 (19.5)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED        45       29         0         21          3          4
  7Q GAIN WILD-TYPE     128       58         3         41          6          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q GAIN MUTATED          1         0         0
  7Q GAIN WILD-TYPE        1         1         2
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 45               128
  STAGE II                29                58
  STAGE III                0                 3
  STAGE IIIA              21                41
  STAGE IIIB               3                 6
  STAGE IIIC               4                 3
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q GAIN MUTATED    48  34  25   3
  7Q GAIN WILD-TYPE 135  61  52   9
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              48               135
  T2              34                61
  T3              25                52
  T4               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    72   2
  7Q GAIN WILD-TYPE 182   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     72    2
  7Q GAIN WILD-TYPE  182    1
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              72               182
  1               2                 1
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    76   1
  7Q GAIN WILD-TYPE 190   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     76    1
  7Q GAIN WILD-TYPE  190    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              76               190
  1               1                 3
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    35  75
  7Q GAIN WILD-TYPE  83 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     35   75
  7Q GAIN WILD-TYPE   83  177
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              35                83
  MALE                75               177
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   100   4
  7Q GAIN WILD-TYPE 238   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    100    4
  7Q GAIN WILD-TYPE  238    5
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              100               238
  YES               4                 5
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7Q GAIN MUTATED                         0                      109
  7Q GAIN WILD-TYPE                       3                      251
                   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                 3
  HEPATOCELLULAR CARCINOMA                     109               251
  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    97   5   0   6
  7Q GAIN WILD-TYPE 227  12   1  15
D14V10, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              97               227
  R1               5                12
  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                                  2    40
  7Q GAIN WILD-TYPE                                0   118
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           6    61
  7Q GAIN WILD-TYPE                        11   122
D14V11, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                         40               118
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         61               122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     7 100
  7Q GAIN WILD-TYPE   9 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7  100
  7Q GAIN WILD-TYPE    9  235
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 9
  NOT HISPANIC OR LATINO             100               235
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    45  26
  8P GAIN WILD-TYPE 190 103
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               71               293 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               26               103 
$`8P GAIN MUTATED`
TCGA-EP-A3JL TCGA-MI-A75H TCGA-2Y-A9GW TCGA-2Y-A9H1 TCGA-5C-A9VG TCGA-5C-A9VH 
        9.96        24.56        41.79        40.41        10.78        10.59 
TCGA-5R-AA1D TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MB 
       14.76        46.78         4.24         3.35         3.32        10.36 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-DD-A119 TCGA-DD-A11A 
       11.41         8.94        21.34        12.00         7.33         2.60 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A3A1 TCGA-DD-A4NN 
       90.71        19.79        12.95         6.02         7.66        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-AAC8 TCGA-DD-AACD 
       73.81        12.26         0.30        80.75         0.53        12.53 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACT TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 
       53.19        69.11        51.35         5.62        18.54        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADU TCGA-DD-AAE1 
       44.22        22.09        40.47        39.52        18.21        18.15 
TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAW2 TCGA-ED-A459 
       18.61        35.08        80.71        56.48        60.99        29.92 
TCGA-ED-A66Y TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC 
        9.73        13.15        13.41         1.84        19.59         0.62 
TCGA-FV-A4ZQ TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M7 
        0.39        58.49        21.53        22.95        20.42        11.87 
TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-GJ-A3OU TCGA-K7-AAU7 TCGA-KR-A7K2 
       15.78        11.80        13.55        28.90        11.80        27.25 
TCGA-RC-A6M4 TCGA-UB-A7MC TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
        0.72        16.44         0.99        12.99        20.22 

$`8P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-UB-A7MF 
       20.75         2.14        31.27        12.72         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       10.32        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 
       63.75        80.28        24.89        27.88       120.82        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       49.84        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 
        8.55        13.02         0.66        17.10         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        14.60        12.72        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 
        0.66         2.86         3.19         3.39         4.24         9.86 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7II 
        9.96        11.93         9.99         7.13         9.83        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-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
      113.00         0.46        21.76        51.29        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        11.47        45.11        49.15        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-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78        30.61        33.14        32.52        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NV TCGA-DD-A73A 
       30.51        39.78        56.25       108.76        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-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE 
       13.48        11.41        75.65        76.41        55.40        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       12.00        15.42         6.41         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
       42.81        61.68        13.64        14.20        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD3 
       50.33        46.82         5.59        47.67         4.50        42.58 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADG 
       40.08        40.54        40.83        13.97         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-AADW 
       14.89        15.06        14.33        66.67        15.58        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.25        18.25        20.98        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       15.72        25.08        26.63        25.78        50.33        90.48 
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-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       62.47        66.25        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-A7XO 
       13.91        13.35         0.20        12.82         0.20        14.04 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK 
       13.35         0.20        18.74        19.99        20.61        11.93 
TCGA-ES-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-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV2 
       17.10        14.70        20.78        14.14        15.65        12.23 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89        11.64         2.14        11.87         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-LG-A9QC 
        2.99        37.71        17.06        16.83        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        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-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       15.52        36.10        27.88        19.76         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       10.75        11.34        24.85        18.28        33.86        30.41 
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-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.30              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            90.71            120.82 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            16.44             20.75 
[1] "0.3 - 90.7 (16.4)"  "0.0 - 120.8 (20.8)"
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P GAIN MUTATED        36       17         0         14          1          1
  8P GAIN WILD-TYPE     137       70         3         48          8          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P GAIN MUTATED          1         0         0
  8P GAIN WILD-TYPE        1         1         2
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 36               137
  STAGE II                17                70
  STAGE III                0                 3
  STAGE IIIA              14                48
  STAGE IIIB               1                 8
  STAGE IIIC               1                 6
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P GAIN MUTATED    36  17  17   2
  8P GAIN WILD-TYPE 147  78  60  10
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              36               147
  T2              17                78
  T3              17                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"
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    56   0
  8P GAIN WILD-TYPE 198   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     56    0
  8P GAIN WILD-TYPE  198    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              56               198
  1               0                 3
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    58   1
  8P GAIN WILD-TYPE 208   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     58    1
  8P GAIN WILD-TYPE  208    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              58               208
  1               1                 3
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    18  55
  8P GAIN WILD-TYPE 100 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     18   55
  8P GAIN WILD-TYPE  100  197
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              18               100
  MALE                55               197
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    61   4
  8P GAIN WILD-TYPE 277   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     61    4
  8P GAIN WILD-TYPE  277    5
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               61               277
  YES               4                 5
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8P GAIN MUTATED                         0                       71
  8P GAIN WILD-TYPE                       3                      289
                   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                        0                 3
  HEPATOCELLULAR CARCINOMA                      71               289
  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    62   2   1   6
  8P GAIN WILD-TYPE 262  15   0  15
D15V10, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              62               262
  R1               2                15
  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
  8P GAIN MUTATED                                  1    37
  8P GAIN WILD-TYPE                                1   121
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           2    31
  8P GAIN WILD-TYPE                        15   152
D15V11, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                         37               121
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         31               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"
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3  67
  8P GAIN WILD-TYPE  13 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   67
  8P GAIN WILD-TYPE   13  268
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              67               268
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   118  62
  8Q GAIN WILD-TYPE 117  67
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              180               184 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               62                67 
$`8Q GAIN MUTATED`
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE8 TCGA-DD-AAEG 
       36.66         0.36        90.28        26.83        21.83        23.64 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
        9.96        22.62         8.12         6.38        81.73        30.74 
TCGA-G3-A3CG TCGA-KR-A7K7 TCGA-MI-A75H TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9H1 
       22.13        31.27        24.56        41.79        24.89        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG 
       56.91        47.74        18.25         1.18        13.02        10.78 
TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10U 
       10.59        17.10        14.76        48.99        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A3KF TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5264 TCGA-CC-A1HT 
        2.99         0.26        14.60         4.24         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IF 
        9.86        10.36        11.93        11.41         8.94        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV 
        9.83        12.00        13.12         8.61         4.60         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        6.94         8.15        79.73        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF 
        2.60        21.76        90.71        19.79        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       45.11         6.02        13.64        21.14         5.62        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
        7.66        17.59        30.97        30.51        29.56        73.81 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AAC8 
       12.26         0.30        80.75        22.78       114.35         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACG TCGA-DD-AACH 
       11.41        75.65        76.41        12.53        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       53.19        69.11        58.16        42.81        61.68        13.64 
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-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADK 
       40.83        13.97        40.47        39.52        35.67        34.49 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU 
        0.39        29.52        14.89        14.33        66.67        18.21 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEE TCGA-DD-AAEI 
       18.25        18.15        18.61        23.74        26.63        50.33 
TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       35.08        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        60.99        53.69        29.92 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
       13.35         9.73         0.20        13.15        13.41         1.84 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A2QQ TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CJ 
       23.97         0.39        51.06        58.49        21.53        19.53 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       25.25        22.95        20.42        20.78        11.87        15.78 
TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-K7-A6G5 
       11.80        13.55        11.64        28.90         2.99        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       11.80        27.25        12.03         9.57        16.67        20.71 
TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A6M4 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
       10.85        17.69         0.72        19.04        15.39        36.10 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       16.44         1.71        15.98        10.75         0.99        12.99 
TCGA-WX-AA44 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       20.22        13.55        35.77        12.99        45.57        11.21 

$`8Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-G3-A6UC TCGA-G3-A7M9 
       17.98        18.87        21.17        18.90        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       20.75         2.14        12.72         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU 
       29.52         0.69        40.80        23.80        53.39        63.75 
TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       80.28        27.88       120.82        49.84        20.81        22.92 
TCGA-2Y-A9HB TCGA-5C-AAPD TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
        8.55         0.66         1.51        27.91        37.32        10.13 
TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
       27.52        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        12.72        18.48        44.81        13.45         0.66 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A5UD 
        2.86         3.19         3.39         4.24         9.96         9.99 
TCGA-CC-A7IE TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HU TCGA-DD-A114 TCGA-DD-A115 
        7.13        12.56         9.14        11.31        37.78        83.57 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH 
        0.46        51.29        79.40        66.31        75.65        49.15 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A2 
       33.04        18.35        27.19        55.69        25.81        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NV 
       32.52        30.15        39.78        56.25       108.76        78.84 
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-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACQ 
       55.40        71.80        12.00         0.30         3.52        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-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADF TCGA-DD-AADG 
        4.50        42.58        40.08        40.54         3.78        37.64 
TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADP TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY 
       35.05        20.91        15.06        15.58        19.30        18.25 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH 
       20.98        19.99         4.64        15.72        25.08        25.78 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-ED-A4XI TCGA-ED-A5KG 
       90.48        89.69        82.62        72.39        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K 
       13.91         0.20        12.82        14.04        13.35         0.20 
TCGA-EP-A26S TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       19.99        60.89        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH 
        0.33        13.68        53.79        28.27        14.86        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M8 TCGA-G3-AAV0 
        5.92        19.23        17.10        14.70        14.14        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       12.23         0.89         2.14        11.87         1.02         2.20 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-MI-A75G TCGA-MR-A520 
       37.71        17.06        29.79        13.97        22.95         7.53 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A6M6 
       58.88        26.27        21.01         3.09         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-WJ-A86L 
       21.04        19.33        15.52        27.88        19.76        11.34 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CY 
       24.85        18.28        33.86        30.41        22.78        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZS-A9CF 
       23.21        35.87        25.15        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 
           18.575            20.945 
[1] "0.2 - 114.3 (18.6)" "0.0 - 120.8 (20.9)"
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED        84       52         0         33          3          2
  8Q GAIN WILD-TYPE      89       35         3         29          6          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q GAIN MUTATED          2         0         0
  8Q GAIN WILD-TYPE        0         1         2
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 84                89
  STAGE II                52                35
  STAGE III                0                 3
  STAGE IIIA              33                29
  STAGE IIIB               3                 6
  STAGE IIIC               2                 5
  STAGE IV                 2                 0
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED   86 55 38  4
  8Q GAIN WILD-TYPE 97 40 39  8
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              86                97
  T2              55                40
  T3              38                39
  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   134   0
  8Q GAIN WILD-TYPE 120   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    134    0
  8Q GAIN WILD-TYPE  120    3
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             134               120
  1               0                 3
[1] 2 2
[1] FALSE
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   135   2
  8Q GAIN WILD-TYPE 131   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    135    2
  8Q GAIN WILD-TYPE  131    2
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             135               131
  1               2                 2
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    44 140
  8Q GAIN WILD-TYPE  74 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     44  140
  8Q GAIN WILD-TYPE   74  112
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              44                74
  MALE               140               112
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   164   7
  8Q GAIN WILD-TYPE 174   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    164    7
  8Q GAIN WILD-TYPE  174    2
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              164               174
  YES               7                 2
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8Q GAIN MUTATED                         1                      181
  8Q GAIN WILD-TYPE                       2                      179
                   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                 2
  HEPATOCELLULAR CARCINOMA                     181               179
  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   160   9   1  11
  8Q GAIN WILD-TYPE 164   8   0  10
D16V10, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             160               164
  R1               9                 8
  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                                  2    88
  8Q GAIN WILD-TYPE                                0    70
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          10    79
  8Q GAIN WILD-TYPE                         7   104
D16V11, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                         88                70
  BLACK OR AFRICAN AMERICAN                     10                 7
  WHITE                                         79               104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     7 169
  8Q GAIN WILD-TYPE   9 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      7  169
  8Q GAIN WILD-TYPE    9  166
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 9
  NOT HISPANIC OR LATINO             169               166
[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 223 123
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               18               346 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6               123 
$`9P GAIN MUTATED`
TCGA-ZP-A9D1 TCGA-5C-AAPD TCGA-5R-AA1C TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A7II 
        0.69         0.66        17.10         0.66         3.35        13.12 
TCGA-CC-A7IK TCGA-CC-A8HV TCGA-DD-A3A7 TCGA-DD-A4NV TCGA-DD-AACB TCGA-DD-AADJ 
        8.61         9.17        13.78        78.84        76.41        35.05 
TCGA-DD-AAVV TCGA-ED-A66Y TCGA-ED-A7XO TCGA-EP-A2KB TCGA-G3-A25U TCGA-KR-A7K2 
       80.71         9.73        14.04        19.59        53.79        27.25 

$`9P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS 
        0.76         7.04        10.32        29.52        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       10.59        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 
       14.60        12.72        18.48        44.81        13.45         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-A7IL 
        7.13        21.34         9.83        12.00        12.56         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
        4.60        11.31         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-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11        30.61        33.14        32.52 
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-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 
       71.80        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-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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.20        12.82         0.20        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-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-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        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-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        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        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        17.06        16.83        11.80        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       12.99        45.57        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 
           13.910            20.055 
[1] "0.7 - 80.7 (13.9)"  "0.0 - 120.8 (20.1)"
[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     168       83         3         55          8          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P GAIN MUTATED          1         0         0
  9P GAIN WILD-TYPE        1         1         2
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  5               168
  STAGE II                 4                83
  STAGE III                0                 3
  STAGE IIIA               7                55
  STAGE IIIB               1                 8
  STAGE IIIC               0                 7
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P GAIN MUTATED     6   5   8   0
  9P GAIN WILD-TYPE 177  90  69  12
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               6               177
  T2               5                90
  T3               8                69
  T4               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    16   0
  9P GAIN WILD-TYPE 238   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     16    0
  9P GAIN WILD-TYPE  238    3
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              16               238
  1               0                 3
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    15   1
  9P GAIN WILD-TYPE 251   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15    1
  9P GAIN WILD-TYPE  251    3
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              15               251
  1               1                 3
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     8  11
  9P GAIN WILD-TYPE 110 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      8   11
  9P GAIN WILD-TYPE  110  241
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               8               110
  MALE                11               241
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    19   0
  9P GAIN WILD-TYPE 319   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     19    0
  9P GAIN WILD-TYPE  319    9
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               19               319
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9P GAIN MUTATED                         0                       17
  9P GAIN WILD-TYPE                       3                      343
                   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                 3
  HEPATOCELLULAR CARCINOMA                      17               343
  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 308  17   1  18
D17V10, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              16               308
  R1               0                17
  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                                2   147
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           1     6
  9P GAIN WILD-TYPE                        16   177
D17V11, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         11               147
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                          6               177
[1] 4 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  15 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   16
  9P GAIN WILD-TYPE   15  319
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              16               319
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    11   7
  9Q GAIN WILD-TYPE 224 122
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               18               346 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7               122 
$`9Q GAIN MUTATED`
TCGA-ZP-A9D1 TCGA-2Y-A9GY TCGA-5R-AA1C TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A7II 
        0.69        24.89        17.10         0.66         3.35        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        27.25         0.99 

$`9Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS 
        0.76         7.04        10.32        29.52        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        63.75        41.79        80.28        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       40.41        56.91        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        10.78        10.59 
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-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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 
       14.60        12.72        18.48        44.81        13.45         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-A7IL 
        7.13        21.34         9.83        12.00        12.56         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
        4.60        11.31         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-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74        13.78        30.61        33.14        32.52 
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-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        71.80        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-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-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-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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         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-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       20.61         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        28.27        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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        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-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 
        2.99        37.71        17.06        16.83        11.80        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        36.10        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B 
       16.44         1.71        15.98        10.75        11.34        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       12.99        45.57        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 
           18.345            19.890 
[1] "0.7 - 107.1 (18.3)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1"  
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q GAIN MUTATED         5        5         0          6          0          0
  9Q GAIN WILD-TYPE     168       82         3         56          9          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q GAIN MUTATED          1         0         0
  9Q GAIN WILD-TYPE        1         1         2
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  5               168
  STAGE II                 5                82
  STAGE III                0                 3
  STAGE IIIA               6                56
  STAGE IIIB               0                 9
  STAGE IIIC               0                 7
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q GAIN MUTATED     6   6   7   0
  9Q GAIN WILD-TYPE 177  89  70  12
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               6               177
  T2               6                89
  T3               7                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"
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    14   0
  9Q GAIN WILD-TYPE 240   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     14    0
  9Q GAIN WILD-TYPE  240    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              14               240
  1               0                 3
[1] 2 2
[1] FALSE
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    14   1
  9Q GAIN WILD-TYPE 252   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     14    1
  9Q GAIN WILD-TYPE  252    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              14               252
  1               1                 3
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    10   9
  9Q GAIN WILD-TYPE 108 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     10    9
  9Q GAIN WILD-TYPE  108  243
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              10               108
  MALE                 9               243
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    19   0
  9Q GAIN WILD-TYPE 319   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     19    0
  9Q GAIN WILD-TYPE  319    9
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               19               319
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9Q GAIN MUTATED                         0                       18
  9Q GAIN WILD-TYPE                       3                      342
                   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                 3
  HEPATOCELLULAR CARCINOMA                      18               342
  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    16   0   0   3
  9Q GAIN WILD-TYPE 308  17   1  18
D18V10, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              16               308
  R1               0                17
  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     9
  9Q GAIN WILD-TYPE                                2   149
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           1     9
  9Q GAIN WILD-TYPE                        16   174
D18V11, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          9               149
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                          9               174
[1] 4 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  17
  9Q GAIN WILD-TYPE  15 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   17
  9Q GAIN WILD-TYPE   15  318
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              17               318
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    34  22
  10P GAIN WILD-TYPE 201 107
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                56                308 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                107 
$`10P GAIN MUTATED`
TCGA-DD-AADV TCGA-DD-AAE8 TCGA-ES-A2HS TCGA-2Y-A9GS TCGA-2Y-A9HA TCGA-3K-AAZ8 
       18.87        21.83        22.62        23.80         1.18        13.02 
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10R TCGA-CC-5264 TCGA-CC-A3MB TCGA-CC-A5UC 
       10.78        37.32        10.13         3.35        10.36        11.41 
TCGA-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW 
        9.99         9.83        12.00        11.31         9.17         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A1EL TCGA-DD-A3A9 TCGA-DD-A4NV TCGA-DD-A73D 
       79.73        37.78        13.64        30.61        78.84        22.78 
TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AADF 
      114.35        76.41         5.62        44.22        40.47         3.78 
TCGA-DD-AADN TCGA-DD-AADW TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAED TCGA-DD-AAEK 
       29.52        19.30        18.61        23.74        25.08        35.08 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A4ZQ 
       29.92        13.35        13.41         1.84        19.59         0.39 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-MR-A8JO 
       22.95        20.42        17.10        11.64         2.14        10.85 
TCGA-NI-A8LF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7ME TCGA-UB-AA0U 
       26.27        15.39        15.52        27.88        15.98        10.75 
TCGA-XR-A8TF TCGA-YA-A8S7 
       22.78        13.55 

$`10P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 
       17.98        36.66         0.36        90.28        26.83        21.17 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       18.90        23.64         9.96         8.12         6.38        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       30.74        22.13        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       31.27        12.72        24.56         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       29.52         0.69        40.80        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       80.28        24.89        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB 
       49.84        47.74        18.25        20.81        22.92         8.55 
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-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       14.60        12.72        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        4.24         2.86         3.19         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        9.86         9.96        11.93         8.94         7.13        21.34 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A9FS 
       13.12        12.56         8.61         9.14         4.60         6.94 
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-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       33.04        18.35        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        13.78        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       23.05         1.45        35.67        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       75.65        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-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-AAEB TCGA-DD-AAEE TCGA-DD-AAEH 
       20.98        19.99         4.64        15.72        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        90.48        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        60.99        53.69        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-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-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       12.03         0.03         0.33        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.53        19.23        25.25        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        0.89        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
        7.53        58.88        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 
        0.49         0.30        21.04        19.33        19.04        36.10 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       19.76        16.44         1.71        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-ZP-A9CV 
       20.22        24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       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 
            16.540             20.415 
[1] "0.4 - 114.3 (16.5)" "0.0 - 120.8 (20.4)"
[1] "hr=" "1.4"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10P GAIN MUTATED        22       16         0         14          1
  10P GAIN WILD-TYPE     151       71         3         48          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P GAIN MUTATED            0        1         0         1
  10P GAIN WILD-TYPE          7        1         1         1
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  22                151
  STAGE II                 16                 71
  STAGE III                 0                  3
  STAGE IIIA               14                 48
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED    22  19  16   1
  10P GAIN WILD-TYPE 161  76  61  11
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               22                161
  T2               19                 76
  T3               16                 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"
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    40   0
  10P GAIN WILD-TYPE 214   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     40    0
  10P GAIN WILD-TYPE  214    3
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               40                214
  1                0                  3
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    41   2
  10P GAIN WILD-TYPE 225   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     41    2
  10P GAIN WILD-TYPE  225    2
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               41                225
  1                2                  2
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    18  40
  10P GAIN WILD-TYPE 100 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     18   40
  10P GAIN WILD-TYPE  100  212
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               18                100
  MALE                 40                212
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    52   2
  10P GAIN WILD-TYPE 286   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     52    2
  10P GAIN WILD-TYPE  286    7
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                52                286
  YES                2                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10P GAIN MUTATED                         1                       56
  10P GAIN WILD-TYPE                       2                      304
                    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                  2
  HEPATOCELLULAR CARCINOMA                       56                304
  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    51   3   0   4
  10P GAIN WILD-TYPE 273  14   1  17
D19V10, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               51                273
  R1                3                 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 GAIN MUTATED                                  0    30
  10P GAIN WILD-TYPE                                2   128
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           3    25
  10P GAIN WILD-TYPE                        14   158
D19V11, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          30                128
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          25                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"
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     4  53
  10P GAIN WILD-TYPE  12 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4   53
  10P GAIN WILD-TYPE   12  282
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 12
  NOT HISPANIC OR LATINO               53                282
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    24  10
  10Q GAIN WILD-TYPE 211 119
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                34                330 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                119 
$`10Q GAIN MUTATED`
TCGA-DD-AADV TCGA-ES-A2HS TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-CC-A7IG TCGA-CC-A7IH 
       18.87        22.62        13.02        10.78         9.83        12.00 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A39Z TCGA-DD-A3A9 
       11.31         9.17         8.15        79.73        19.76        30.61 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AADD TCGA-DD-AADN TCGA-DD-AAE9 
       78.84       114.35        76.41        40.47        29.52        23.74 
TCGA-DD-AAED TCGA-DD-AAEK TCGA-ED-A66X TCGA-ED-A82E TCGA-EP-A2KB TCGA-FV-A4ZQ 
       25.08        35.08        13.35        13.41        19.59         0.39 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-NI-A8LF TCGA-RC-A7SH 
       20.42        17.10        11.64         2.14        26.27        15.39 
TCGA-UB-A7MA TCGA-UB-AA0U TCGA-XR-A8TF TCGA-YA-A8S7 
       27.88        10.75        22.78        13.55 

$`10Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 
       17.98        36.66         0.36        90.28        26.83        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64         9.96         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       10.32        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       63.75        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       40.41        56.91        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
       22.92         1.18         8.55        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       12.72        18.48        44.81        13.45         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-A7IE TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
        8.94         7.13        21.34        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        9.14         4.60         6.94        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-A3A0 
       13.64        21.14        27.19        55.69         5.62        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       13.78        33.14        32.52        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        35.67        13.48         0.53        11.41        75.65 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        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-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.54        40.83        13.97        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO 
       35.67        35.05        34.49        20.91         0.39        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
        4.64        15.72        26.63        25.78        50.33        90.48 
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        60.99 
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-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-A2KC 
        1.84         0.20        18.74        19.99        20.61         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       12.03         0.03         0.33        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M5 TCGA-G3-A7M6 
       19.53        19.23        25.25        22.95        14.70        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-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       13.55         0.89        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       19.04        15.52        36.10        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       18.28        33.86        30.41        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        79.30        11.21 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.39               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            114.35             120.82 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             19.23              19.99 
[1] "0.4 - 114.3 (19.2)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.2"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q GAIN MUTATED        12       12         0          9          1
  10Q GAIN WILD-TYPE     161       75         3         53          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q GAIN MUTATED            0        1         0         1
  10Q GAIN WILD-TYPE          7        1         1         1
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  12                161
  STAGE II                 12                 75
  STAGE III                 0                  3
  STAGE IIIA                9                 53
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED    12  13  10   1
  10Q GAIN WILD-TYPE 171  82  67  11
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               12                171
  T2               13                 82
  T3               10                 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"
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    25   0
  10Q GAIN WILD-TYPE 229   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     25    0
  10Q GAIN WILD-TYPE  229    3
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               25                229
  1                0                  3
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    26   2
  10Q GAIN WILD-TYPE 240   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     26    2
  10Q GAIN WILD-TYPE  240    2
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               26                240
  1                2                  2
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    13  23
  10Q GAIN WILD-TYPE 105 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     13   23
  10Q GAIN WILD-TYPE  105  229
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               13                105
  MALE                 23                229
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    30   1
  10Q GAIN WILD-TYPE 308   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     30    1
  10Q GAIN WILD-TYPE  308    8
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                30                308
  YES                1                  8
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10Q GAIN MUTATED                         0                       35
  10Q GAIN WILD-TYPE                       3                      325
                    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                  3
  HEPATOCELLULAR CARCINOMA                       35                325
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    32   2   0   2
  10Q GAIN WILD-TYPE 292  15   1  19
D20V10, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               32                292
  R1                2                 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
  10Q GAIN MUTATED                                  0    16
  10Q GAIN WILD-TYPE                                2   142
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           1    18
  10Q GAIN WILD-TYPE                        16   165
D20V11, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          16                142
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                          18                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"
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3  32
  10Q GAIN WILD-TYPE  13 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3   32
  10Q GAIN WILD-TYPE   13  303
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               32                303
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    12   5
  11P GAIN WILD-TYPE 223 124
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                347 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                124 
$`11P GAIN MUTATED`
TCGA-G3-A3CG TCGA-LG-A6GG TCGA-2Y-A9GZ TCGA-BC-A69H TCGA-BD-A3EP TCGA-CC-A7IE 
       22.13        12.72        27.88        14.60        13.45         7.13 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-AAD1 
       13.12        12.56         7.33         5.62        78.84        18.54 
TCGA-ED-A66Y TCGA-ED-A82E TCGA-FV-A4ZQ TCGA-UB-A7ME TCGA-WQ-A9G7 
        9.73        13.41         0.39        15.98         0.99 

$`11P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 
        8.12         6.38        81.73        30.74        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
       20.75         2.14        31.27        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       10.32        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        41.79        80.28        24.89       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       56.91        49.84        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       12.72        18.48        44.81         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-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
       21.34         9.83        12.00         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-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-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 
       71.80        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-AAD2 TCGA-DD-AAD3 
        5.59        47.67         5.62         4.50        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-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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        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        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.91        13.35         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        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        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
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-AA0U TCGA-WJ-A86L 
       27.88        19.76        16.44         1.71        10.75        11.34 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
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-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        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 
             13.12              20.42 
[1] "0.4 - 78.8 (13.1)"  "0.0 - 120.8 (20.4)"
[1] "hr=" "1.4"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P GAIN MUTATED         7        4         0          5          0
  11P GAIN WILD-TYPE     166       83         3         57          9
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P GAIN MUTATED            0        1         0         0
  11P GAIN WILD-TYPE          7        1         1         2
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   7                166
  STAGE II                  4                 83
  STAGE III                 0                  3
  STAGE IIIA                5                 57
  STAGE IIIB                0                  9
  STAGE IIIC                0                  7
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED     7   4   7   0
  11P GAIN WILD-TYPE 176  91  70  12
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                7                176
  T2                4                 91
  T3                7                 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"
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    10   0
  11P GAIN WILD-TYPE 244   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10    0
  11P GAIN WILD-TYPE  244    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               10                244
  1                0                  3
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    14   1
  11P GAIN WILD-TYPE 252   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     14    1
  11P GAIN WILD-TYPE  252    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               14                252
  1                1                  3
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     7  11
  11P GAIN WILD-TYPE 111 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7   11
  11P GAIN WILD-TYPE  111  241
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                7                111
  MALE                 11                241
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    15   0
  11P GAIN WILD-TYPE 323   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     15    0
  11P GAIN WILD-TYPE  323    9
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                15                323
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11P GAIN MUTATED                         0                       18
  11P GAIN WILD-TYPE                       3                      342
                    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                  3
  HEPATOCELLULAR CARCINOMA                       18                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
  11P GAIN MUTATED    14   2   1   1
  11P GAIN WILD-TYPE 310  15   0  20
D21V10, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               14                310
  R1                2                 15
  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     9
  11P GAIN WILD-TYPE                                2   149
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           1     8
  11P GAIN WILD-TYPE                        16   175
D21V11, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           9                149
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           8                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"
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  18
  11P GAIN WILD-TYPE  16 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   18
  11P GAIN WILD-TYPE   16  317
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               18                317
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    13   6
  11Q GAIN WILD-TYPE 222 123
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                19                345 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                123 
$`11Q GAIN MUTATED`
TCGA-G3-A3CG TCGA-LG-A6GG TCGA-2Y-A9GZ TCGA-BC-A69I TCGA-BD-A3EP TCGA-CC-A7IE 
       22.13        12.72        27.88        12.72        13.45         7.13 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NV 
       13.12        12.56         7.33         5.62        25.81        78.84 
TCGA-DD-AAD1 TCGA-DD-AADW TCGA-DD-AAE0 TCGA-ED-A66Y TCGA-ED-A82E TCGA-FV-A4ZQ 
       18.54        19.30        18.25         9.73        13.41         0.39 
TCGA-WQ-A9G7 
        0.99 

$`11Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 
        8.12         6.38        81.73        30.74        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
       20.75         2.14        31.27        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       10.32        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        41.79        80.28        24.89       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       56.91        49.84        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       14.60        18.48        44.81         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-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
       21.34         9.83        12.00         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-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       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-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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78        30.61        33.14        32.52        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-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        80.75        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
       47.67         5.62         4.50        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
       66.67        15.58        18.21        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        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        60.99        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-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-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       12.03         0.03         0.33        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
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-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 
        1.71        15.98        10.75        11.34        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        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 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.39               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             78.84             120.82 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.12              20.42 
[1] "0.4 - 78.8 (13.1)"  "0.0 - 120.8 (20.4)"
[1] "hr=" "1.4"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED         9        3         0          6          0
  11Q GAIN WILD-TYPE     164       84         3         56          9
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q GAIN MUTATED            0        1         0         0
  11Q GAIN WILD-TYPE          7        1         1         2
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   9                164
  STAGE II                  3                 84
  STAGE III                 0                  3
  STAGE IIIA                6                 56
  STAGE IIIB                0                  9
  STAGE IIIC                0                  7
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED     9   3   8   0
  11Q GAIN WILD-TYPE 174  92  69  12
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                9                174
  T2                3                 92
  T3                8                 69
  T4                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    13   0
  11Q GAIN WILD-TYPE 241   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     13    0
  11Q GAIN WILD-TYPE  241    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               13                241
  1                0                  3
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    17   1
  11Q GAIN WILD-TYPE 249   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     17    1
  11Q GAIN WILD-TYPE  249    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               17                249
  1                1                  3
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     8  12
  11Q GAIN WILD-TYPE 110 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      8   12
  11Q GAIN WILD-TYPE  110  240
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                8                110
  MALE                 12                240
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    17   0
  11Q GAIN WILD-TYPE 321   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     17    0
  11Q GAIN WILD-TYPE  321    9
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                17                321
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11Q GAIN MUTATED                         0                       20
  11Q GAIN WILD-TYPE                       3                      340
                    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                  3
  HEPATOCELLULAR CARCINOMA                       20                340
  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    16   2   1   1
  11Q GAIN WILD-TYPE 308  15   0  20
D22V10, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               16                308
  R1                2                 15
  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    10
  11Q GAIN WILD-TYPE                                2   148
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           1     9
  11Q GAIN WILD-TYPE                        16   174
D22V11, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          10                148
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           9                174
[1] 4 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  19
  11Q GAIN WILD-TYPE  16 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   19
  11Q GAIN WILD-TYPE   16  316
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               19                316
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    24  15
  12P GAIN WILD-TYPE 211 114
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                39                325 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                114 
$`12P GAIN MUTATED`
TCGA-EP-A3JL TCGA-G3-A7M9 TCGA-2Y-A9GW TCGA-2Y-A9H2 TCGA-5C-A9VG TCGA-BW-A5NO 
        9.96         1.84        41.79        56.91        10.78         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-A3A7 TCGA-DD-A4NR TCGA-DD-A73G 
        8.15         2.60        12.95        13.78         0.30       114.35 
TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACZ TCGA-DD-AADF TCGA-DD-AADR TCGA-ED-A66Y 
       53.19         0.30         5.62         3.78        66.67         9.73 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-AAV1 
        0.20         0.20        13.41        27.88        51.06        11.80 
TCGA-G3-AAV6 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75C TCGA-NI-A8LF TCGA-UB-A7MA 
        2.14        11.80        27.25         9.57        26.27        27.88 
TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-XR-A8TF 
       15.98         0.99        22.78 

$`12P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
        6.38        81.73        30.74        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       10.32        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        80.28        24.89        27.88       120.82        40.41 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       49.84        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55        13.02        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
       44.42        45.93         0.26        22.36        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       18.48        44.81        13.45         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-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.93         9.99         8.94        21.34         9.83        12.00 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 
        8.61         9.14         4.60         9.17         6.94        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        11.47        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05        22.78         1.45        35.67        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM 
       12.00        15.42         6.41        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-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG 
       40.54        40.83        13.97        40.47        39.52        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-AADS TCGA-DD-AADU TCGA-DD-AADW 
       14.89        15.06        14.33        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        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        60.99        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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       19.10        12.03         0.03         0.33         0.39        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-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        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        11.64        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75E TCGA-MI-A75G 
       16.83        29.79        13.97        12.03        16.67        22.95 
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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        15.52        36.10        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
        1.71        10.75        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       18.28        33.86        30.41        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 

  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 
             11.41              20.75 
[1] "0.2 - 114.3 (11.4)" "0.0 - 120.8 (20.8)"
[1] "hr=" "1.6"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P GAIN MUTATED        16        9         0         11          2
  12P GAIN WILD-TYPE     157       78         3         51          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P GAIN MUTATED            1        0         0         0
  12P GAIN WILD-TYPE          6        2         1         2
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  16                157
  STAGE II                  9                 78
  STAGE III                 0                  3
  STAGE IIIA               11                 51
  STAGE IIIB                2                  7
  STAGE IIIC                1                  6
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P GAIN MUTATED    16   9  14   1
  12P GAIN WILD-TYPE 167  86  63  11
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               16                167
  T2                9                 86
  T3               14                 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"
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    29   0
  12P GAIN WILD-TYPE 225   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     29    0
  12P GAIN WILD-TYPE  225    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               29                225
  1                0                  3
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    31   0
  12P GAIN WILD-TYPE 235   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     31    0
  12P GAIN WILD-TYPE  235    4
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               31                235
  1                0                  4
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    15  25
  12P GAIN WILD-TYPE 103 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     15   25
  12P GAIN WILD-TYPE  103  227
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               15                103
  MALE                 25                227
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    37   0
  12P GAIN WILD-TYPE 301   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     37    0
  12P GAIN WILD-TYPE  301    9
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                37                301
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12P GAIN MUTATED                         0                       36
  12P GAIN WILD-TYPE                       3                      324
                    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                  3
  HEPATOCELLULAR CARCINOMA                       36                324
  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    35   1   0   3
  12P GAIN WILD-TYPE 289  16   1  18
D23V10, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               35                289
  R1                1                 16
  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                                  1    18
  12P GAIN WILD-TYPE                                1   140
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           2    18
  12P GAIN WILD-TYPE                        15   165
D23V11, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          18                140
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          18                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"
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1  36
  12P GAIN WILD-TYPE  15 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   36
  12P GAIN WILD-TYPE   15  299
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               36                299
[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 205 113
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                46                318 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                113 
$`12Q GAIN MUTATED`
TCGA-DD-A4ND TCGA-EP-A3JL TCGA-G3-A7M9 TCGA-2Y-A9GW TCGA-2Y-A9H0 TCGA-2Y-A9H2 
       90.28         9.96         1.84        41.79       120.82        56.91 
TCGA-5C-A9VG TCGA-BC-A3KF TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A5UC TCGA-CC-A7IE 
       10.78         0.26         0.66         3.35        11.41         7.13 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A11A TCGA-DD-A1EF 
       13.12        12.56        11.31         8.15         2.60        12.95 
TCGA-DD-A1EJ TCGA-DD-A3A7 TCGA-DD-A4NH TCGA-DD-A4NR TCGA-DD-A73G TCGA-DD-AACI 
       33.04        13.78        30.15         0.30       114.35        53.19 
TCGA-DD-AACK TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AADR TCGA-DD-AAEI TCGA-DD-AAVV 
        0.30        47.67         5.62        66.67        50.33        80.71 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-FV-A3I0 TCGA-G3-A25T 
        9.73         0.20         0.20        13.41        27.88        51.06 
TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75C TCGA-NI-A8LF 
       11.80         2.14        11.80        27.25         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-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 
       81.73        30.74        22.13        22.06        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       31.27        12.72        24.56         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU 
       29.52         0.69        40.80        23.80        53.39        63.75 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       80.28        24.89        27.88        40.41        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
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-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        14.60        12.72        18.48        44.81        13.45 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        4.24         2.86         3.19         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.86         9.96        10.36        11.93         9.99         8.94 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
       21.34         9.83        12.00         8.61         9.14         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-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65        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-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-A3A9 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       32.52        30.97        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 
       71.80        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-AAD0 
       51.35        51.52        50.33        46.82         5.59         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        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-AADS TCGA-DD-AADU 
       29.52        14.89        15.06        14.33        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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        35.08        90.48        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        60.99        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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
       12.03         0.03         0.33         0.39        13.68        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
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-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       12.23        13.55         0.89        11.64        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       29.79        13.97        12.03        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A6M4 
        7.53        10.85        58.88        17.69         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.75        11.34        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       33.86        30.41        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        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             20.320 
[1] "0.2 - 120.8 (12.8)" "0.0 - 113.0 (20.3)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q GAIN MUTATED        19        9         0         12          4
  12Q GAIN WILD-TYPE     154       78         3         50          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q GAIN MUTATED            2        0         0         0
  12Q GAIN WILD-TYPE          5        2         1         2
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  19                154
  STAGE II                  9                 78
  STAGE III                 0                  3
  STAGE IIIA               12                 50
  STAGE IIIB                4                  5
  STAGE IIIC                2                  5
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q GAIN MUTATED    20   9  16   2
  12Q GAIN WILD-TYPE 163  86  61  10
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               20                163
  T2                9                 86
  T3               16                 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"
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    34   1
  12Q GAIN WILD-TYPE 220   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     34    1
  12Q GAIN WILD-TYPE  220    2
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               34                220
  1                1                  2
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    38   0
  12Q GAIN WILD-TYPE 228   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     38    0
  12Q GAIN WILD-TYPE  228    4
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               38                228
  1                0                  4
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    18  29
  12Q GAIN WILD-TYPE 100 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     18   29
  12Q GAIN WILD-TYPE  100  223
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               18                100
  MALE                 29                223
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    43   0
  12Q GAIN WILD-TYPE 295   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     43    0
  12Q GAIN WILD-TYPE  295    9
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                43                295
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12Q GAIN MUTATED                         0                       44
  12Q GAIN WILD-TYPE                       3                      316
                    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                  3
  HEPATOCELLULAR CARCINOMA                       44                316
  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    42   0   0   3
  12Q GAIN WILD-TYPE 282  17   1  18
D24V10, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               42                282
  R1                0                 17
  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                                  1    20
  12Q GAIN WILD-TYPE                                1   138
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           2    23
  12Q GAIN WILD-TYPE                        15   160
D24V11, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          20                138
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          23                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"
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  41
  12Q GAIN WILD-TYPE  14 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   41
  12Q GAIN WILD-TYPE   14  294
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               41                294
[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 224 118
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                342 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                11                118 
$`13Q GAIN MUTATED`
TCGA-EP-A3JL TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-BC-A3KF TCGA-BD-A3EP TCGA-CC-5263 
        9.96        41.79        27.88         0.26        13.45         4.24 
TCGA-CC-A7IE TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A3A7 TCGA-DD-AACB TCGA-DD-AACO 
        7.13        45.11        33.04        13.78        76.41        61.68 
TCGA-DD-AAE3 TCGA-DD-AAVW TCGA-ED-A66Y TCGA-FV-A23B TCGA-G3-AAV1 TCGA-G3-AAV6 
       18.61        76.18         9.73        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-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       53.39        63.75        80.28        24.89       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       56.91        49.84        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        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-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
       23.38         1.12        44.42        45.93        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       12.72        18.48        44.81         0.66         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.19         3.39         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-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-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        12.95        49.15         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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        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 
       71.80        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-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-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.25        18.15        20.98        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
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        60.99 
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-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR 
       19.59         0.62        11.93        14.40        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        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-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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        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        11.64 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.72         0.49         0.30        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       15.52        27.88        19.76         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
       11.34         0.99        12.99        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        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             19.775 
[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     162       84         3         57          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q GAIN MUTATED            2        1         0         0
  13Q GAIN WILD-TYPE          5        1         1         2
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  11                162
  STAGE II                  3                 84
  STAGE III                 0                  3
  STAGE IIIA                5                 57
  STAGE IIIB                1                  8
  STAGE IIIC                2                  5
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED    12   4   6   1
  13Q GAIN WILD-TYPE 171  91  71  11
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               12                171
  T2                4                 91
  T3                6                 71
  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 236   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     18    1
  13Q GAIN WILD-TYPE  236    2
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               18                236
  1                1                  2
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    17   1
  13Q GAIN WILD-TYPE 249   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     17    1
  13Q GAIN WILD-TYPE  249    3
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               17                249
  1                1                  3
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    11  12
  13Q GAIN WILD-TYPE 107 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     11   12
  13Q GAIN WILD-TYPE  107  240
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               11                107
  MALE                 12                240
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    21   1
  13Q GAIN WILD-TYPE 317   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     21    1
  13Q GAIN WILD-TYPE  317    8
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                21                317
  YES                1                  8
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  13Q GAIN MUTATED                         0                       23
  13Q GAIN WILD-TYPE                       3                      337
                    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                  3
  HEPATOCELLULAR CARCINOMA                       23                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
  13Q GAIN MUTATED    19   0   0   3
  13Q GAIN WILD-TYPE 305  17   1  18
D25V10, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               19                305
  R1                0                 17
  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                                2   149
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           2    11
  13Q GAIN WILD-TYPE                        15   172
D25V11, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           9                149
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          11                172
[1] 4 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  14 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2   19
  13Q GAIN WILD-TYPE   14  316
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               19                316
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    12  10
  14Q GAIN WILD-TYPE 223 119
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                342 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                10                119 
$`14Q GAIN MUTATED`
TCGA-DD-A4ND TCGA-ES-A2HS TCGA-G3-A3CG TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H2 
       90.28        22.62        22.13        41.79        27.88        56.91 
TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-A3M9 TCGA-DD-A114 
       20.81        13.02        44.81        13.45         9.86        37.78 
TCGA-DD-A119 TCGA-DD-AACB TCGA-DD-AAE3 TCGA-ED-A66Y TCGA-ED-A7XO TCGA-FV-A3I0 
        7.33        76.41        18.61         9.73        14.04        27.88 
TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-UB-A7ME TCGA-YA-A8S7 
        2.14        27.25        15.98        13.55 

$`14Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64         9.96         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       81.73        30.74        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       31.27        12.72        24.56         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU 
       29.52         0.69        40.80        23.80        53.39        63.75 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       80.28        24.89       120.82        40.41        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH 
       18.25        22.92         1.18         8.55        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-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5258 
       22.36        14.60        12.72        18.48         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-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-A7II TCGA-CC-A7IJ 
        7.13        21.34         9.83        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-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-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       75.65        55.40        12.53        71.80        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-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-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       20.98        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        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        60.99        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-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       12.82         0.20        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 
       11.93        14.40        60.89        23.97        19.10        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
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-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
       11.80        12.23        13.55         0.89        11.64        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       16.83        11.80        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0U 
       36.10        27.88        19.76        16.44         1.71        10.75 
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-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       33.86        30.41        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        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 
             21.47              19.76 
[1] "2.1 - 90.3 (21.5)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q GAIN MUTATED        10        3         0          5          1
  14Q GAIN WILD-TYPE     163       84         3         57          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q GAIN MUTATED            0        1         0         0
  14Q GAIN WILD-TYPE          7        1         1         2
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  10                163
  STAGE II                  3                 84
  STAGE III                 0                  3
  STAGE IIIA                5                 57
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED    11   4   7   0
  14Q GAIN WILD-TYPE 172  91  70  12
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               11                172
  T2                4                 91
  T3                7                 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"
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    14   0
  14Q GAIN WILD-TYPE 240   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     14    0
  14Q GAIN WILD-TYPE  240    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               14                240
  1                0                  3
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    12   1
  14Q GAIN WILD-TYPE 254   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     12    1
  14Q GAIN WILD-TYPE  254    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               12                254
  1                1                  3
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     9  13
  14Q GAIN WILD-TYPE 109 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      9   13
  14Q GAIN WILD-TYPE  109  239
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                9                109
  MALE                 13                239
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    20   0
  14Q GAIN WILD-TYPE 318   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     20    0
  14Q GAIN WILD-TYPE  318    9
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                20                318
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  14Q GAIN MUTATED                         0                       20
  14Q GAIN WILD-TYPE                       3                      340
                    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                  3
  HEPATOCELLULAR CARCINOMA                       20                340
  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    19   1   1   1
  14Q GAIN WILD-TYPE 305  16   0  20
D26V10, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               19                305
  R1                1                 16
  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     7
  14Q GAIN WILD-TYPE                                2   151
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           3    12
  14Q GAIN WILD-TYPE                        14   171
D26V11, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           7                151
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          12                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"
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  19
  14Q GAIN WILD-TYPE  15 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   19
  14Q GAIN WILD-TYPE   15  316
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               19                316
[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 212 119
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                331 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                119 
$`15Q GAIN MUTATED`
TCGA-DD-A4NI TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-ES-A2HS TCGA-G3-A6UC TCGA-2Y-A9GS 
       26.83        21.83        18.90        22.62        22.06        23.80 
TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10Y 
       27.88        56.91         8.55        10.78        37.32        23.38 
TCGA-BC-A3KG TCGA-CC-A3M9 TCGA-CC-A5UE TCGA-CC-A7IF TCGA-DD-A4NV TCGA-DD-A73G 
       22.36         9.86         8.94        21.34        78.84       114.35 
TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAEK 
       76.41        13.64         5.62        18.21        18.61        35.08 
TCGA-ED-A66X TCGA-ED-A8O6 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-MI-A75G 
       13.35         1.84         0.39        51.06        58.49        22.95 
TCGA-MR-A8JO TCGA-RC-A7SK TCGA-WQ-AB4B 
       10.85        15.52        12.99 

$`15Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        90.28        18.87        21.17 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
       23.64         9.96         8.12         6.38        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG 
       22.13         1.84        20.75         2.14        31.27        12.72 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 
       24.56         0.76         7.04        10.32        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       40.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
      120.82        40.41        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
       22.92         1.18        13.02        10.59         0.66        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S 
       14.76         1.51        48.99        27.91        10.13        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A216 
       27.52        27.52         2.99        25.32         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       45.93         0.26        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45         0.66         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-A7IE TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
       11.41         9.99         7.13         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-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05        22.78         1.45        35.67        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       11.41        75.65        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       58.16        42.81        61.68        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        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        90.48        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        60.99        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-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       13.68        53.79        28.27        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-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        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        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        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-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.75        11.34         0.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        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 

  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              19.76 
[1] "0.4 - 114.3 (21.8)" "0.0 - 120.8 (19.8)"
[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     160       78         3         56          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q GAIN MUTATED            0        0         0         0
  15Q GAIN WILD-TYPE          7        2         1         2
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  13                160
  STAGE II                  9                 78
  STAGE III                 0                  3
  STAGE IIIA                6                 56
  STAGE IIIB                2                  7
  STAGE IIIC                0                  7
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED    13  11   7   2
  15Q GAIN WILD-TYPE 170  84  70  10
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               13                170
  T2               11                 84
  T3                7                 70
  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 230   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     24    0
  15Q GAIN WILD-TYPE  230    3
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               24                230
  1                0                  3
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    25   0
  15Q GAIN WILD-TYPE 241   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     25    0
  15Q GAIN WILD-TYPE  241    4
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               25                241
  1                0                  4
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     9  24
  15Q GAIN WILD-TYPE 109 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9   24
  15Q GAIN WILD-TYPE  109  228
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                9                109
  MALE                 24                228
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    31   0
  15Q GAIN WILD-TYPE 307   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     31    0
  15Q GAIN WILD-TYPE  307    9
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                31                307
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  15Q GAIN MUTATED                         1                       32
  15Q GAIN WILD-TYPE                       2                      328
                    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                  2
  HEPATOCELLULAR CARCINOMA                       32                328
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    31   1   0   1
  15Q GAIN WILD-TYPE 293  16   1  20
D27V10, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               31                293
  R1                1                 16
  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                                2   143
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           0    17
  15Q GAIN WILD-TYPE                        17   166
D27V11, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          15                143
  BLACK OR AFRICAN AMERICAN                       0                 17
  WHITE                                          17                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"
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2  30
  15Q GAIN WILD-TYPE  14 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2   30
  15Q GAIN WILD-TYPE   14  305
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               30                305
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    24   8
  16P GAIN WILD-TYPE 211 121
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                32                332 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 8                121 
$`16P GAIN MUTATED`
TCGA-BC-A112 TCGA-2Y-A9GY TCGA-3K-AAZ8 TCGA-5R-AA1D TCGA-BC-A10R TCGA-CC-A7IK 
        5.03        24.89        13.02        14.76        10.13         8.61 
TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1EL TCGA-DD-A3A5 TCGA-DD-AACI TCGA-DD-AACS 
       79.73         2.60        13.64       102.74        53.19        59.31 
TCGA-DD-AACT TCGA-DD-AADN TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAVV TCGA-DD-AAW0 
       51.35        29.52        18.61        19.99        80.71        66.25 
TCGA-ED-A459 TCGA-ED-A7PZ TCGA-ED-A82E TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SM 
       29.92         0.20        13.41        13.68        51.06        17.10 
TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-RC-A6M5 TCGA-UB-A7MB 
       11.80        27.25        10.85        26.27         0.49        19.76 
TCGA-UB-AA0U TCGA-XR-A8TE 
       10.75        30.41 

$`16P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        63.75        41.79        80.28        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       40.41        56.91        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
       22.92         1.18         8.55        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
       17.10         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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
       44.42        45.93         0.26        22.36        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       18.48        44.81        13.45         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-A7II TCGA-CC-A7IJ 
        7.13        21.34         9.83        12.00        13.12        12.56 
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-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       33.04        18.35        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-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        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        71.80        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-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       14.20        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-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-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-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       20.98         4.64        23.74        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        90.48        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-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        60.99        53.69        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         9.73         0.20        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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
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-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-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       16.83        11.80        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V 
       16.67        22.95        20.71         7.53        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
       21.01         3.09         0.72         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
       19.04        15.39        15.52        36.10        27.88        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
        1.71        15.98        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       24.85        18.28        33.86        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-A9CF TCGA-ZS-A9CG 
       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 
            19.185             19.890 
[1] "0.2 - 102.7 (19.2)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1.5"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED        11       10         1          5          1
  16P GAIN WILD-TYPE     162       77         2         57          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P GAIN MUTATED            1        0         1         0
  16P GAIN WILD-TYPE          6        2         0         2
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  11                162
  STAGE II                 10                 77
  STAGE III                 1                  2
  STAGE IIIA                5                 57
  STAGE IIIB                1                  8
  STAGE IIIC                1                  6
  STAGE IV                  0                  2
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P GAIN MUTATED    12  10   9   1
  16P GAIN WILD-TYPE 171  85  68  11
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               12                171
  T2               10                 85
  T3                9                 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"
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    21   1
  16P GAIN WILD-TYPE 233   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     21    1
  16P GAIN WILD-TYPE  233    2
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               21                233
  1                1                  2
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    22   0
  16P GAIN WILD-TYPE 244   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     22    0
  16P GAIN WILD-TYPE  244    4
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               22                244
  1                0                  4
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    10  22
  16P GAIN WILD-TYPE 108 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     10   22
  16P GAIN WILD-TYPE  108  230
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               10                108
  MALE                 22                230
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    28   2
  16P GAIN WILD-TYPE 310   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     28    2
  16P GAIN WILD-TYPE  310    7
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                28                310
  YES                2                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16P GAIN MUTATED                         2                       29
  16P GAIN WILD-TYPE                       1                      331
                    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                         2                  1
  HEPATOCELLULAR CARCINOMA                       29                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
  16P GAIN MUTATED    28   2   0   2
  16P GAIN WILD-TYPE 296  15   1  19
D28V10, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               28                296
  R1                2                 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
  16P GAIN MUTATED                                  0    13
  16P GAIN WILD-TYPE                                2   145
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           3    16
  16P GAIN WILD-TYPE                        14   167
D28V11, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          13                145
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          16                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"
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  28
  16P GAIN WILD-TYPE  15 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   28
  16P GAIN WILD-TYPE   15  307
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               28                307
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    13   4
  16Q GAIN WILD-TYPE 222 125
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                17                347 
  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-RC-A6M5 TCGA-XR-A8TE TCGA-YA-A8S7 
       27.25        10.85         0.49        30.41        13.55 

$`16Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.76         7.04        10.32        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG 
       18.25        20.81        22.92         1.18         8.55        10.78 
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-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-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        14.60        12.72        18.48        44.81        13.45 
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-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.35         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-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-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-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        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        71.80        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-AACU TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        59.31        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49        20.91         0.39        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-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-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.25        18.15        20.98        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       90.48        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        60.99 
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-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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        53.79        28.27        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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       20.42        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-AAV6 
       15.65        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       17.06        16.83        11.80        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 
        9.57        16.67        22.95        20.71         7.53        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M6 
       26.27        17.69        21.01         3.09         0.72         0.30 
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-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
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-A8TD TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       33.86        22.78        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.49               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] "0.5 - 80.7 (14.8)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.3"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED         5        3         0          6          1
  16Q GAIN WILD-TYPE     168       84         3         56          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q GAIN MUTATED            1        0         1         0
  16Q GAIN WILD-TYPE          6        2         0         2
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   5                168
  STAGE II                  3                 84
  STAGE III                 0                  3
  STAGE IIIA                6                 56
  STAGE IIIB                1                  8
  STAGE IIIC                1                  6
  STAGE IV                  0                  2
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q GAIN MUTATED     6   3   7   1
  16Q GAIN WILD-TYPE 177  92  70  11
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                6                177
  T2                3                 92
  T3                7                 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"
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    13   1
  16Q GAIN WILD-TYPE 241   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     13    1
  16Q GAIN WILD-TYPE  241    2
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               13                241
  1                1                  2
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    12   0
  16Q GAIN WILD-TYPE 254   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     12    0
  16Q GAIN WILD-TYPE  254    4
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               12                254
  1                0                  4
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     5  12
  16Q GAIN WILD-TYPE 113 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5   12
  16Q GAIN WILD-TYPE  113  240
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                5                113
  MALE                 12                240
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    15   1
  16Q GAIN WILD-TYPE 323   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     15    1
  16Q GAIN WILD-TYPE  323    8
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                15                323
  YES                1                  8
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16Q GAIN MUTATED                         2                       14
  16Q GAIN WILD-TYPE                       1                      346
                    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                         2                  1
  HEPATOCELLULAR CARCINOMA                       14                346
  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    15   0   0   2
  16Q GAIN WILD-TYPE 309  17   1  19
D29V10, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               15                309
  R1                0                 17
  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                                2   151
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           2     8
  16Q GAIN WILD-TYPE                        15   175
D29V11, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           7                151
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                           8                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"
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2  12
  16Q GAIN WILD-TYPE  14 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   12
  16Q GAIN WILD-TYPE   14  323
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               12                323
[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 216 118
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                30                334 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                11                118 
$`17P GAIN MUTATED`
TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25W TCGA-3K-AAZ8 TCGA-BC-A10Q TCGA-BW-A5NO 
       22.62        81.73        30.74        13.02        37.32         0.66 
TCGA-CC-A3M9 TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A3A7 
        9.86         7.13         9.83         8.15        37.78        13.78 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACI 
       73.81       108.76        22.78        11.41        76.41        53.19 
TCGA-DD-AACS TCGA-DD-AAD0 TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AAE3 TCGA-ED-A66X 
       59.31         4.50        44.22        40.47        18.61        13.35 
TCGA-ED-A66Y TCGA-EP-A2KB TCGA-G3-AAV6 TCGA-NI-A8LF TCGA-UB-A7MA TCGA-UB-AA0U 
        9.73        19.59         2.14        26.27        27.88        10.75 

$`17P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
        6.38        22.13        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       31.27        12.72        24.56         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU 
       29.52         0.69        40.80        23.80        53.39        63.75 
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       41.79        80.28        24.89        27.88       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       56.91        49.84        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        1.18         8.55        10.78        10.59         0.66        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S 
       14.76         1.51        48.99        27.91        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
       44.42        45.93         0.26        22.36        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       18.48        44.81        13.45         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-A5UE TCGA-CC-A7IF TCGA-CC-A7IH 
       11.93        11.41         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-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        9.17         6.94        79.73        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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       30.61        33.14        32.52        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93         9.30        23.05         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
      114.35        13.48         0.53        75.65        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       71.80        12.00        15.42         6.41        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
        5.62        18.54        21.63        42.58        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.54        40.83        13.97        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        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        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       28.08        13.91         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-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       19.99        20.61         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.39        13.68        51.06        53.79        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-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-A7M5 TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10        14.70        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-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       13.55         0.89        11.64        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       22.95        20.71         7.53        10.85        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB 
       19.33        19.04        15.39        15.52        36.10        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       16.44         1.71        15.98        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       12.99        45.57        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 
            21.105             19.775 
[1] "0.7 - 108.8 (21.1)" "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     161       81         3         54          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P GAIN MUTATED            0        0         0         0
  17P GAIN WILD-TYPE          7        2         1         2
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  12                161
  STAGE II                  6                 81
  STAGE III                 0                  3
  STAGE IIIA                8                 54
  STAGE IIIB                3                  6
  STAGE IIIC                0                  7
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED    12   7  11   0
  17P GAIN WILD-TYPE 171  88  66  12
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               12                171
  T2                7                 88
  T3               11                 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"
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    20   0
  17P GAIN WILD-TYPE 234   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     20    0
  17P GAIN WILD-TYPE  234    3
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               20                234
  1                0                  3
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    22   0
  17P GAIN WILD-TYPE 244   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     22    0
  17P GAIN WILD-TYPE  244    4
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               22                244
  1                0                  4
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     9  21
  17P GAIN WILD-TYPE 109 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      9   21
  17P GAIN WILD-TYPE  109  231
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                9                109
  MALE                 21                231
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    29   0
  17P GAIN WILD-TYPE 309   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     29    0
  17P GAIN WILD-TYPE  309    9
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                29                309
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17P GAIN MUTATED                         0                       29
  17P GAIN WILD-TYPE                       3                      331
                    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                  3
  HEPATOCELLULAR CARCINOMA                       29                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
  17P GAIN MUTATED    24   4   0   2
  17P GAIN WILD-TYPE 300  13   1  19
D30V10, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               24                300
  R1                4                 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
  17P GAIN MUTATED                                  0    14
  17P GAIN WILD-TYPE                                2   144
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           3    12
  17P GAIN WILD-TYPE                        14   171
D30V11, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          14                144
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          12                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"
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  29
  17P GAIN WILD-TYPE  16 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   29
  17P GAIN WILD-TYPE   16  306
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               29                306
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    59  33
  17Q GAIN WILD-TYPE 176  96
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                92                272 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                33                 96 
$`17Q GAIN MUTATED`
TCGA-BC-A112 TCGA-DD-AAEA TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25W TCGA-XR-A8TG 
        5.03        18.90        22.62        81.73        30.74        29.52 
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-A217 TCGA-BC-A69H 
       48.99        37.32         2.99        23.38        45.93        14.60 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3MC 
        0.66         2.86         3.19         4.24         3.35        11.93 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IK 
       11.41         8.94         7.13        21.34         9.83         8.61 
TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EI 
        8.15        37.78         7.33         2.60        79.40         6.02 
TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NO TCGA-DD-A4NP 
        5.62        17.59        13.78        30.61        73.81       108.76 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE 
       22.78         1.45        11.41        75.65        76.41        71.80 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD5 
       53.19        69.11        59.31         5.59         4.50        44.22 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADO TCGA-DD-AADR 
       13.97        40.47        39.52        37.64        14.89        66.67 
TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAVV TCGA-DD-AAW1 TCGA-ED-A66X 
       18.21        18.61        26.63        80.71        65.39        13.35 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A495 
        9.73         0.20         1.84        19.59         0.62         0.03 
TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-AAUZ 
       53.79        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 
       11.64         2.14        22.95        20.71        26.27        17.69 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0U TCGA-WJ-A86L TCGA-XR-A8TD TCGA-ZP-A9CZ 
       27.88        16.44        10.75        11.34        33.86        23.21 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.15        12.99 

$`17Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A3CG 
       21.83        23.64         9.96         8.12         6.38        22.13 
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG 
       22.06         1.84        20.75         2.14        31.27        12.72 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       24.56         0.76         7.04        10.32         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       23.80        53.39        63.75        41.79        80.28        27.88 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA 
       40.41        49.84        47.74        18.25        20.81         1.18 
TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55        10.78        10.59         0.66        17.10        14.76 
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-A10Z TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO 
        1.12        44.42         0.26        22.36        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
       44.81        13.45         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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
       20.12       102.74       107.11        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ 
       30.15        30.51        39.78        56.25        29.56        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACC TCGA-DD-AACD 
       35.67       114.35        13.48         0.53        55.40        12.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       12.00        15.42         6.41         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU 
       42.81        61.68        13.64        14.20        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 
       50.33        46.82        47.67         5.62        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADF 
       42.58        22.09        40.08        40.54        40.83         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       15.06        14.33        15.58        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15        20.98        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        25.78        50.33        35.08        90.48        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-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       62.47        66.25        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       28.08        13.91         0.20        12.82        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41        13.35         0.20        18.74        19.99        20.61 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
       12.03         0.33         0.39        13.68        51.06        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI 
       58.49        14.86        25.64         5.92        19.53        25.25 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV0 
       20.42        17.10        14.70        11.87        14.14        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       11.80        12.23        13.55         0.89        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 
       16.67         7.53        10.85        58.88        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       15.39        15.52        36.10        19.76         1.71        15.98 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE 
        0.99        12.99        20.22        24.85        18.28        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZS-A9CD 
       22.78        13.55        35.77        25.71        35.87        45.57 
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 
            19.065             19.990 
[1] "0.0 - 120.8 (19.1)" "0.2 - 114.3 (20.0)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED        38       20         0         19          5
  17Q GAIN WILD-TYPE     135       67         3         43          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q GAIN MUTATED            1        1         0         1
  17Q GAIN WILD-TYPE          6        1         1         1
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  38                135
  STAGE II                 20                 67
  STAGE III                 0                  3
  STAGE IIIA               19                 43
  STAGE IIIB                5                  4
  STAGE IIIC                1                  6
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED    40  23  25   5
  17Q GAIN WILD-TYPE 143  72  52   7
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               40                143
  T2               23                 72
  T3               25                 52
  T4                5                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    63   0
  17Q GAIN WILD-TYPE 191   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     63    0
  17Q GAIN WILD-TYPE  191    3
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               63                191
  1                0                  3
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    67   2
  17Q GAIN WILD-TYPE 199   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     67    2
  17Q GAIN WILD-TYPE  199    2
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               67                199
  1                2                  2
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    23  70
  17Q GAIN WILD-TYPE  95 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     23   70
  17Q GAIN WILD-TYPE   95  182
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               23                 95
  MALE                 70                182
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    83   2
  17Q GAIN WILD-TYPE 255   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     83    2
  17Q GAIN WILD-TYPE  255    7
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                83                255
  YES                2                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17Q GAIN MUTATED                         0                       92
  17Q GAIN WILD-TYPE                       3                      268
                    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                  3
  HEPATOCELLULAR CARCINOMA                       92                268
  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 246  10   0  14
D31V10, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               78                246
  R1                7                 10
  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                                2   110
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           6    36
  17Q GAIN WILD-TYPE                        11   147
D31V11, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          48                110
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          36                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"
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     5  86
  17Q GAIN WILD-TYPE  11 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5   86
  17Q GAIN WILD-TYPE   11  249
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 11
  NOT HISPANIC OR LATINO               86                249
[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 211 118
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                35                329 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                11                118 
$`18P GAIN MUTATED`
TCGA-2Y-A9H7 TCGA-EP-A3JL TCGA-FV-A4ZP TCGA-ZP-A9D1 TCGA-2Y-A9GS TCGA-2Y-A9GY 
       38.40         9.96        81.73         0.69        23.80        24.89 
TCGA-2Y-A9H2 TCGA-3K-AAZ8 TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3MC TCGA-CC-A5UC 
       56.91        13.02         0.66         4.24        11.93        11.41 
TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        9.83        13.12        12.56         6.94         8.15        79.73 
TCGA-DD-A119 TCGA-DD-A4NN TCGA-DD-AACF TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
        7.33        29.56        12.00        13.97        40.47         3.78 
TCGA-DD-AADJ TCGA-DD-AADR TCGA-DD-AAE9 TCGA-DD-AAVP TCGA-ED-A66X TCGA-G3-A25T 
       35.05        66.67        23.74        90.48        13.35        51.06 
TCGA-G3-A25X TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-ZP-A9CZ 
       58.49        15.39        36.10         0.99        23.21 

$`18P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64        22.62         8.12         6.38 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       30.74        22.13        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       31.27        12.72        24.56         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       29.52        40.80        53.39        63.75        41.79        80.28 
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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH 
       20.81        22.92         1.18         8.55        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-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        14.60        12.72        18.48        44.81        13.45 
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-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        9.17        37.78        83.57        53.33       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-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-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-AACG TCGA-DD-AACH 
       76.41        55.40        12.53        71.80        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-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK 
       40.54        40.83        39.52        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-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-AAEB TCGA-DD-AAED 
       20.98        18.61        19.99         4.64        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR 
       26.63        25.78        50.33        35.08        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        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       26.93        28.08        13.91         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
       12.03         0.03         0.33         0.39        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-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       19.23        25.25        22.95        20.42        17.10        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        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK 
        0.49         0.30        21.04        19.33        19.04        15.52 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
       11.34        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
       30.41        22.78        13.55        35.77        25.71        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.66               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             90.48             120.82 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             13.97              19.99 
[1] "0.7 - 90.5 (14.0)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.1"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P GAIN MUTATED        12        9         0          9          1
  18P GAIN WILD-TYPE     161       78         3         53          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P GAIN MUTATED            0        1         0         0
  18P GAIN WILD-TYPE          7        1         1         2
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  12                161
  STAGE II                  9                 78
  STAGE III                 0                  3
  STAGE IIIA                9                 53
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED    14  10  12   0
  18P GAIN WILD-TYPE 169  85  65  12
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               14                169
  T2               10                 85
  T3               12                 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"
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    27   0
  18P GAIN WILD-TYPE 227   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     27    0
  18P GAIN WILD-TYPE  227    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               27                227
  1                0                  3
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    26   1
  18P GAIN WILD-TYPE 240   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     26    1
  18P GAIN WILD-TYPE  240    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               26                240
  1                1                  3
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    10  26
  18P GAIN WILD-TYPE 108 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     10   26
  18P GAIN WILD-TYPE  108  226
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               10                108
  MALE                 26                226
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    34   0
  18P GAIN WILD-TYPE 304   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     34    0
  18P GAIN WILD-TYPE  304    9
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                34                304
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18P GAIN MUTATED                         0                       36
  18P GAIN WILD-TYPE                       3                      324
                    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                  3
  HEPATOCELLULAR CARCINOMA                       36                324
  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    30   1   1   3
  18P GAIN WILD-TYPE 294  16   0  18
D32V10, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               30                294
  R1                1                 16
  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                                  1    21
  18P GAIN WILD-TYPE                                1   137
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           3    11
  18P GAIN WILD-TYPE                        14   172
D32V11, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          21                137
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          11                172
[1] 4 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  15 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   34
  18P GAIN WILD-TYPE   15  301
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               34                301
[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 218 119
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                27                337 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                119 
$`18Q GAIN MUTATED`
TCGA-EP-A3JL TCGA-FV-A4ZP TCGA-ZP-A9D1 TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H2 
        9.96        81.73         0.69        23.80        24.89        56.91 
TCGA-3K-AAZ8 TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A7IG 
       13.02         0.66         4.24        11.93        11.41         9.83 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN 
       13.12        12.56         8.15        79.73         7.33        29.56 
TCGA-DD-AACF TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADJ TCGA-DD-AADR TCGA-DD-AAE3 
       12.00        13.97        40.47        35.05        66.67        18.61 
TCGA-G3-A25T TCGA-G3-A25X TCGA-RC-A7SH 
       51.06        58.49        15.39 

$`18Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64        22.62         8.12 
TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       10.32        29.52        40.80        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       80.28        27.88       120.82        40.41        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG 
       18.25        20.81        22.92         1.18         8.55        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-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
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-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 
       13.45         4.24         2.86         3.19         3.39         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A5UE 
        3.32         9.86         9.96        10.36         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
        7.13        21.34        12.00         8.61         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
       11.31         9.17         6.94        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-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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78        30.61        33.14        32.52        30.97        30.15 
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        71.80 
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-AADF 
       22.09        40.08        40.54        40.83        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       37.64        35.67        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       14.89        15.06        14.33        15.58        18.21        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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        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        60.99        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-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-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-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33         0.39        13.68        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10        14.70        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-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 
        0.30        21.04        19.33        19.04        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
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-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        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 

  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        7         0          8          1
  18Q GAIN WILD-TYPE     164       80         3         54          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q GAIN MUTATED            0        1         0         0
  18Q GAIN WILD-TYPE          7        1         1         2
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   9                164
  STAGE II                  7                 80
  STAGE III                 0                  3
  STAGE IIIA                8                 54
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED    10   8  10   0
  18Q GAIN WILD-TYPE 173  87  67  12
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               10                173
  T2                8                 87
  T3               10                 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"
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    21   0
  18Q GAIN WILD-TYPE 233   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     21    0
  18Q GAIN WILD-TYPE  233    3
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               21                233
  1                0                  3
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    20   1
  18Q GAIN WILD-TYPE 246   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     20    1
  18Q GAIN WILD-TYPE  246    3
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               20                246
  1                1                  3
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     7  21
  18Q GAIN WILD-TYPE 111 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7   21
  18Q GAIN WILD-TYPE  111  231
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                7                111
  MALE                 21                231
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    26   0
  18Q GAIN WILD-TYPE 312   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     26    0
  18Q GAIN WILD-TYPE  312    9
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                26                312
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18Q GAIN MUTATED                         0                       28
  18Q GAIN WILD-TYPE                       3                      332
                    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                  3
  HEPATOCELLULAR CARCINOMA                       28                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
  18Q GAIN MUTATED    22   1   1   3
  18Q GAIN WILD-TYPE 302  16   0  18
D33V10, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               22                302
  R1                1                 16
  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                                  1    16
  18Q GAIN WILD-TYPE                                1   142
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           2     9
  18Q GAIN WILD-TYPE                        15   174
D33V11, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          16                142
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                           9                174
[1] 4 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  15 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   26
  18Q GAIN WILD-TYPE   15  309
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               26                309
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    35  19
  19P GAIN WILD-TYPE 200 110
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                54                310 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                19                110 
$`19P GAIN MUTATED`
TCGA-DD-A4ND TCGA-ES-A2HS TCGA-ZP-A9D1 TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-3K-AAZ8 
       90.28        22.62         0.69        63.75        41.79        13.02 
TCGA-BC-A10Q TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A7II TCGA-DD-A113 
       37.32        13.45         0.66         3.19        13.12        79.73 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39V 
      113.00         7.33        90.71        19.79        12.95        21.14 
TCGA-DD-A39X TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       55.69        13.78        30.61        29.56        73.81        12.26 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AADF TCGA-DD-AAE0 
       78.84       114.35        51.35        46.82         3.78        18.25 
TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E 
       18.61        35.08         9.73         0.20        14.04        13.41 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A25T 
       19.59         0.62        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        28.90        27.25 
TCGA-MI-A75G TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7MA TCGA-YA-A8S7 
       22.95         0.30        21.04        15.39        27.88        13.55 

$`19P GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64         9.96         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GX 
       10.32        29.52        40.80        23.80        53.39        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
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-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
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-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-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-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ 
        8.94         7.13        21.34         9.83        12.00        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-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B 
        8.15        37.78        83.57        53.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE 
       21.76        51.29        79.40        66.31        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-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-A4NA TCGA-DD-A4NB 
       17.59        20.12       102.74       107.11        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       30.97        30.15        30.51        39.78        56.25       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        35.67        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        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-AACU 
       42.81        61.68        13.64        14.20        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       50.33         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-AADG TCGA-DD-AADI 
       40.83        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-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.25        18.15        20.98        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       15.72        25.08        26.63        25.78        50.33        90.48 
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        60.99 
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-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       18.74        19.99        20.61        11.93        14.40        19.10 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
       12.03         0.03         0.33         0.39        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-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M6 
       19.23        25.25        22.95        20.42        14.70        20.78 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14        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 
       11.64         2.14        11.87         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        17.06        16.83        11.80        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB 
        0.49        19.33        19.04        15.52        36.10        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
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-A9CF TCGA-ZS-A9CG 
       12.99        45.57        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 
            21.090             19.645 
[1] "0.2 - 114.3 (21.1)" "0.0 - 120.8 (19.6)"
[1] "hr=" "1.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P GAIN MUTATED        24       16         0          9          2
  19P GAIN WILD-TYPE     149       71         3         53          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P GAIN MUTATED            0        2         0         1
  19P GAIN WILD-TYPE          7        0         1         1
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  24                149
  STAGE II                 16                 71
  STAGE III                 0                  3
  STAGE IIIA                9                 53
  STAGE IIIB                2                  7
  STAGE IIIC                0                  7
  STAGE IV                  2                  0
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED    25  18  12   1
  19P GAIN WILD-TYPE 158  77  65  11
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               25                158
  T2               18                 77
  T3               12                 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"
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    40   0
  19P GAIN WILD-TYPE 214   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     40    0
  19P GAIN WILD-TYPE  214    3
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               40                214
  1                0                  3
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    40   3
  19P GAIN WILD-TYPE 226   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     40    3
  19P GAIN WILD-TYPE  226    1
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               40                226
  1                3                  1
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    25  31
  19P GAIN WILD-TYPE  93 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     25   31
  19P GAIN WILD-TYPE   93  221
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               25                 93
  MALE                 31                221
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    49   1
  19P GAIN WILD-TYPE 289   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     49    1
  19P GAIN WILD-TYPE  289    8
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                49                289
  YES                1                  8
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19P GAIN MUTATED                         0                       53
  19P GAIN WILD-TYPE                       3                      307
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19P GAIN MUTATED                                  3
  19P GAIN WILD-TYPE                                4
D34V9, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  3
  HEPATOCELLULAR CARCINOMA                       53                307
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    47   3   1   5
  19P GAIN WILD-TYPE 277  14   0  16
D34V10, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               47                277
  R1                3                 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                                  1    17
  19P GAIN WILD-TYPE                                1   141
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           4    33
  19P GAIN WILD-TYPE                        13   150
D34V11, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          17                141
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          33                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"
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  50
  19P GAIN WILD-TYPE  13 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   50
  19P GAIN WILD-TYPE   13  285
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               50                285
[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 190 105
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                69                295 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                24                105 
$`19Q GAIN MUTATED`
TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-ES-A2HS TCGA-ZP-A9D1 TCGA-2Y-A9GU 
       90.28        21.17        18.90        22.62         0.69        63.75 
TCGA-2Y-A9GW TCGA-2Y-A9H3 TCGA-3K-AAZ8 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BD-A3EP 
       41.79        49.84        13.02        37.32        10.13        13.45 
TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A7II TCGA-DD-A113 TCGA-DD-A118 
        0.66         3.19         9.86        13.12        79.73       113.00 
TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A39V 
        7.33        90.71        19.79        12.95        45.11        21.14 
TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV 
       55.69        30.61        29.56        73.81        12.26        78.84 
TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AADB 
      114.35        15.42        13.64        51.35        46.82        40.83 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AAE0 TCGA-DD-AAEK TCGA-DD-AAVV 
       13.97         3.78         0.39        18.25        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-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X 
       60.89        23.97        27.88         0.39        51.06        58.49 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-GJ-A3OU TCGA-KR-A7K2 
       17.10        20.78        11.87        15.65        28.90        27.25 
TCGA-MI-A75G TCGA-NI-A8LF TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7MA 
       22.95        26.27         0.30        21.04        15.39        27.88 
TCGA-UB-A7ME TCGA-WQ-AB4B TCGA-YA-A8S7 
       15.98        12.99        13.55 

$`19Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 
       17.98        36.66         0.36        26.83        18.87        21.83 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
       23.64         9.96         8.12         6.38        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       22.13        22.06         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       12.72        24.56         0.76         7.04        10.32        29.52 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       40.80        23.80        53.39        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
      120.82        40.41        56.91        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
       22.92         1.18         8.55        10.78        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-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.38         1.12 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
       44.42        45.93         0.26        22.36        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
       18.48        44.81         4.24         2.86         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-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-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A 
        6.94         8.15        37.78        83.57        53.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        0.46        21.76        51.29        79.40        66.31        75.65 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       11.47        49.15         6.02        33.04        18.35        13.64 
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-A4NA 
       17.59        20.12       102.74       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-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        71.80        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
       42.81        61.68        14.20        59.31        51.52        50.33 
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-AADD 
       42.58        44.22        22.09        40.08        40.54        40.47 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       39.52        37.64        35.67        35.05        34.49        20.91 
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-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       18.21        19.30        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        90.48        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        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 
       13.91        13.35         0.20        12.82        13.15        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK 
        1.84         0.20        18.74        19.99        20.61        11.93 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S 
       14.40        19.10        12.03         0.03         0.33        13.68 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        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-A7M5 
       19.53        19.23        25.25        22.95        20.42        14.70 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14        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 
       11.64         2.14        11.87         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        17.06        16.83        11.80        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       58.88        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC 
       19.33        19.04        15.52        36.10        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 
        1.71        10.75        11.34         0.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY 
       18.28        33.86        30.41        22.78        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 

  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 
             20.78              19.76 
[1] "0.2 - 114.3 (20.8)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED        33       21         0         10          1
  19Q GAIN WILD-TYPE     140       66         3         52          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q GAIN MUTATED            0        2         0         1
  19Q GAIN WILD-TYPE          7        0         1         1
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  33                140
  STAGE II                 21                 66
  STAGE III                 0                  3
  STAGE IIIA               10                 52
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  2                  0
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED    34  23  13   1
  19Q GAIN WILD-TYPE 149  72  64  11
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               34                149
  T2               23                 72
  T3               13                 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"
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    48   0
  19Q GAIN WILD-TYPE 206   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     48    0
  19Q GAIN WILD-TYPE  206    3
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               48                206
  1                0                  3
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    50   3
  19Q GAIN WILD-TYPE 216   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     50    3
  19Q GAIN WILD-TYPE  216    1
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               50                216
  1                3                  1
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    27  44
  19Q GAIN WILD-TYPE  91 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     27   44
  19Q GAIN WILD-TYPE   91  208
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               27                 91
  MALE                 44                208
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    63   1
  19Q GAIN WILD-TYPE 275   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     63    1
  19Q GAIN WILD-TYPE  275    8
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                63                275
  YES                1                  8
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19Q GAIN MUTATED                         0                       68
  19Q GAIN WILD-TYPE                       3                      292
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19Q GAIN MUTATED                                  3
  19Q GAIN WILD-TYPE                                4
D35V9, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  3
  HEPATOCELLULAR CARCINOMA                       68                292
  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
  19Q GAIN MUTATED    62   3   1   5
  19Q GAIN WILD-TYPE 262  14   0  16
D35V10, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               62                262
  R1                3                 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                                  1    26
  19Q GAIN WILD-TYPE                                1   132
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           4    40
  19Q GAIN WILD-TYPE                        13   143
D35V11, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          26                132
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          40                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"
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     4  65
  19Q GAIN WILD-TYPE  12 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      4   65
  19Q GAIN WILD-TYPE   12  270
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 12
  NOT HISPANIC OR LATINO               65                270
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    57  48
  20P GAIN WILD-TYPE 178  81
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               105                259 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                48                 81 
$`20P GAIN MUTATED`
TCGA-DD-A4ND TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A6UC TCGA-G3-A7M9 
       90.28         9.96        22.62         6.38        22.06         1.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-XR-A8TG TCGA-2Y-A9GS TCGA-2Y-A9GX TCGA-2Y-A9GY 
       31.27        12.72        29.52        23.80        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-5C-A9VH TCGA-5R-AAAM 
       27.88        20.81        22.92         1.18        10.59         1.51 
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H 
       48.99        37.32        10.13        45.93         0.26        14.60 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5264 TCGA-CC-A3M9 
       44.81        13.45         0.66         3.19         3.35         9.86 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A8HU 
       10.36        11.41         8.94         7.13        13.12        11.31 
TCGA-CC-A9FW TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A1EG 
        8.15       113.00         7.33         2.60        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NN 
       49.15        33.04        21.14        13.78        30.61        29.56 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC 
        0.30        78.84       114.35         0.53        76.41        55.40 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACV 
        6.41        53.19        61.68        13.64        51.35        50.33 
TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN 
        5.62        22.09        40.47         3.78        37.64        29.52 
TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 
       14.89        15.58        18.21        19.30        18.25        18.61 
TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVV TCGA-ED-A66X TCGA-ED-A66Y 
       23.74        25.78        35.08        80.71        13.35         9.73 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A4ZQ 
       14.04        13.41         1.84        19.59        60.89         0.39 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-AAV1 
       13.68        58.49        14.86        17.10        20.78        11.80 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-MI-A75G TCGA-NI-A8LF 
        0.89         2.14         2.99        27.25        22.95        26.27 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       36.10        27.88        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-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W 
       21.83        18.90        23.64         8.12        81.73        30.74 
TCGA-G3-A3CG TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
       22.13        20.75         2.14        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       10.32         0.69        40.80        53.39        63.75        41.79 
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-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55        13.02        10.78         0.66        17.10        14.76 
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO 
       23.38         1.12        44.42        22.36        12.72        18.48 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        4.24         2.86         3.39         4.24         3.32         9.96 
TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ 
       11.93         9.99        21.34         9.83        12.00        12.56 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 
        8.61         9.14         4.60         9.17         6.94        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       37.78        83.57        53.33         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-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        18.35        13.64        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      102.74       107.11        33.14        32.52        30.97        30.15 
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        71.80 
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-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       66.67        18.25        18.15        20.98        19.99         4.64 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.72        25.08        26.63        50.33        90.48        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        60.99        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-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       12.03         0.03         0.33        51.06        53.79        28.27 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       22.95        20.42        14.70        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       15.65        12.23        13.55        11.64        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.20        37.71        17.06        16.83        11.80 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       29.79        13.97        12.03         9.57        16.67        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WJ-A86L 
       15.39        15.52        16.44         1.71        15.98        11.34 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-ZP-A9CV 
       20.22        24.85        18.28        33.86        30.41        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       25.71        23.21        35.87        25.15        12.99        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 
             18.25              20.22 
[1] "0.3 - 114.3 (18.2)" "0.0 - 120.8 (20.2)"
[1] "hr=" "1.6"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED        43       26         1         22          4
  20P GAIN WILD-TYPE     130       61         2         40          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P GAIN MUTATED            2        2         0         1
  20P GAIN WILD-TYPE          5        0         1         1
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  43                130
  STAGE II                 26                 61
  STAGE III                 1                  2
  STAGE IIIA               22                 40
  STAGE IIIB                4                  5
  STAGE IIIC                2                  5
  STAGE IV                  2                  0
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P GAIN MUTATED    45  30  29   3
  20P GAIN WILD-TYPE 138  65  48   9
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               45                138
  T2               30                 65
  T3               29                 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"
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    73   1
  20P GAIN WILD-TYPE 181   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     73    1
  20P GAIN WILD-TYPE  181    2
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               73                181
  1                1                  2
[1] 2 2
[1] FALSE
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    80   3
  20P GAIN WILD-TYPE 186   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     80    3
  20P GAIN WILD-TYPE  186    1
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               80                186
  1                3                  1
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    39  68
  20P GAIN WILD-TYPE  79 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     39   68
  20P GAIN WILD-TYPE   79  184
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               39                 79
  MALE                 68                184
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    97   2
  20P GAIN WILD-TYPE 241   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     97    2
  20P GAIN WILD-TYPE  241    7
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                97                241
  YES                2                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20P GAIN MUTATED                         0                      105
  20P GAIN WILD-TYPE                       3                      255
                    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                  3
  HEPATOCELLULAR CARCINOMA                      105                255
  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    95   6   1   4
  20P GAIN WILD-TYPE 229  11   0  17
D36V10, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               95                229
  R1                6                 11
  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
  20P GAIN MUTATED                                  0    45
  20P GAIN WILD-TYPE                                2   113
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           4    56
  20P GAIN WILD-TYPE                        13   127
D36V11, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          45                113
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          56                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"
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     5  95
  20P GAIN WILD-TYPE  11 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5   95
  20P GAIN WILD-TYPE   11  240
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 11
  NOT HISPANIC OR LATINO               95                240
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    63  48
  20Q GAIN WILD-TYPE 172  81
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               111                253 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                48                 81 
$`20Q GAIN MUTATED`
TCGA-DD-A4ND TCGA-DD-AAEA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A6UC 
       90.28        18.90         9.96        22.62         6.38        22.06 
TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-XR-A8TG TCGA-2Y-A9GS TCGA-2Y-A9GX 
        1.84        31.27        12.72        29.52        23.80        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-5C-A9VH 
       24.89        27.88        20.81        22.92         1.18        10.59 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A3KF 
        1.51        48.99        37.32        10.13        45.93         0.26 
TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5264 
       14.60        44.81        13.45         0.66         3.19         3.35 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE 
        9.86        10.36        11.93        11.41         8.94         7.13 
TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A118 TCGA-DD-A119 
       13.12         9.14        11.31         8.15       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
        2.60         0.46        21.76        12.95        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NN TCGA-DD-A4NR 
       33.04        21.14        13.78        30.61        29.56         0.30 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACI 
       78.84       114.35         0.53        76.41        55.40        53.19 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACZ 
       61.68        13.64        59.31        51.35        50.33         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN 
        4.50        22.09        40.47         3.78        37.64        29.52 
TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 
       14.89        15.58        18.21        19.30        18.25        18.61 
TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVV TCGA-ED-A66X TCGA-ED-A66Y 
       23.74        25.78        35.08        80.71        13.35         9.73 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A4ZQ 
       14.04        13.41         1.84        19.59        60.89         0.39 
TCGA-G3-A25S TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-HP-A5MZ 
       13.68        17.10        20.78        11.80         2.14         2.99 
TCGA-KR-A7K2 TCGA-MI-A75G TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RG-A7D4 TCGA-UB-A7MA 
       27.25        22.95        26.27        21.01        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-XR-A8TD 
       19.76        15.98        10.75         0.99        12.99        33.86 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD 
       22.78        13.55        45.57 

$`20Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG 
       21.83        23.64         8.12        81.73        30.74        22.13 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       20.75         2.14        24.56         0.76         7.04        10.32 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9H0 
        0.69        40.80        53.39        63.75        41.79       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9HB 
       40.41        56.91        49.84        47.74        18.25         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4073 
       13.02        10.78         0.66        17.10        14.76        27.91 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-CC-5258 
        1.12        44.42        22.36        12.72        18.48         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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
       20.12       102.74       107.11        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       30.15        30.51        39.78        56.25        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       12.26        80.75        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD 
        1.45        35.67        13.48        11.41        75.65        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       71.80        12.00        15.42         6.41        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW 
        3.52        58.16        42.81        14.20        51.52        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.59        47.67        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-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       66.67        18.25        18.15        20.98        19.99         4.64 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.72        25.08        26.63        50.33        90.48        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        60.99        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-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       12.03         0.03         0.33        51.06        53.79        28.27 
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-A7M5 TCGA-G3-A7M7 
       19.23        25.25        22.95        20.42        14.70        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14        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-A5N0 
       11.64        11.87        28.90         1.02         2.20        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       17.06        16.83        11.80        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        20.71         7.53        10.85        58.88 
TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       17.69         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD 
       19.33        19.04        15.39        15.52        16.44         1.71 
TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-ZP-A9CV 
       11.34        20.22        24.85        18.28        30.41        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       25.71        23.21        35.87        25.15        12.99        79.30 
TCGA-ZS-A9CG 
       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 
             18.61              20.22 
[1] "0.3 - 114.3 (18.6)" "0.0 - 120.8 (20.2)"
[1] "hr=" "1.5"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED        47       24         1         24          6
  20Q GAIN WILD-TYPE     126       63         2         38          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q GAIN MUTATED            2        1         0         1
  20Q GAIN WILD-TYPE          5        1         1         1
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  47                126
  STAGE II                 24                 63
  STAGE III                 1                  2
  STAGE IIIA               24                 38
  STAGE IIIB                6                  3
  STAGE IIIC                2                  5
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q GAIN MUTATED    49  27  32   4
  20Q GAIN WILD-TYPE 134  68  45   8
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               49                134
  T2               27                 68
  T3               32                 45
  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 177   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     77    1
  20Q GAIN WILD-TYPE  177    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               77                177
  1                1                  2
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    85   2
  20Q GAIN WILD-TYPE 181   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     85    2
  20Q GAIN WILD-TYPE  181    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               85                181
  1                2                  2
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    39  73
  20Q GAIN WILD-TYPE  79 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     39   73
  20Q GAIN WILD-TYPE   79  179
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               39                 79
  MALE                 73                179
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   102   2
  20Q GAIN WILD-TYPE 236   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    102    2
  20Q GAIN WILD-TYPE  236    7
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               102                236
  YES                2                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20Q GAIN MUTATED                         0                      110
  20Q GAIN WILD-TYPE                       3                      250
                    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                  3
  HEPATOCELLULAR CARCINOMA                      110                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
  20Q GAIN MUTATED    98   6   1   5
  20Q GAIN WILD-TYPE 226  11   0  16
D37V10, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               98                226
  R1                6                 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
  20Q GAIN MUTATED                                  0    48
  20Q GAIN WILD-TYPE                                2   110
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           4    58
  20Q GAIN WILD-TYPE                        13   125
D37V11, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          48                110
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          58                125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     5 100
  20Q GAIN WILD-TYPE  11 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5  100
  20Q GAIN WILD-TYPE   11  235
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 11
  NOT HISPANIC OR LATINO              100                235
[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 221 118
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                25                339 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                11                118 
$`21Q GAIN MUTATED`
TCGA-ES-A2HS TCGA-G3-A3CG TCGA-2Y-A9GZ TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       22.62        22.13        27.88        20.81        13.02        10.78 
TCGA-BC-A217 TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A5UC TCGA-CC-A7IE 
       45.93         0.66         3.19         4.24        11.41         7.13 
TCGA-CC-A7IG TCGA-DD-A113 TCGA-DD-A3A5 TCGA-DD-A4NV TCGA-DD-AAEK TCGA-ED-A82E 
        9.83        79.73       102.74        78.84        35.08        13.41 
TCGA-EP-A2KB TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-AAUZ TCGA-MI-A75G TCGA-RC-A7SH 
       19.59        27.88        51.06        15.78        22.95        15.39 
TCGA-UB-AA0U 
       10.75 

$`21Q GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        81.73        30.74        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       10.32        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        41.79        80.28        24.89       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       56.91        49.84        47.74        18.25        22.92         1.18 
TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
        8.55        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-A216 
       27.52         2.99        25.32        23.38         1.12        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-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT 
       13.45         4.24         2.86         3.39         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.86         9.96        10.36        11.93         9.99         8.94 
TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
       21.34        12.00        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-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-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-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       107.11        13.78        30.61        33.14        32.52 
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-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        71.80        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-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-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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        90.48        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        60.99        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-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       60.89        23.97        19.10        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        13.68        53.79        28.27        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10        14.70        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-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       29.79        13.97        12.03         9.57        16.67        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
        1.71        15.98        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        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 

  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              19.79 
[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       11         1          7          1
  21Q GAIN WILD-TYPE     168       76         2         55          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q GAIN MUTATED            0        0         0         0
  21Q GAIN WILD-TYPE          7        2         1         2
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   5                168
  STAGE II                 11                 76
  STAGE III                 1                  2
  STAGE IIIA                7                 55
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED     6  11   9   0
  21Q GAIN WILD-TYPE 177  84  68  12
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                6                177
  T2               11                 84
  T3                9                 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"
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    16   0
  21Q GAIN WILD-TYPE 238   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     16    0
  21Q GAIN WILD-TYPE  238    3
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               16                238
  1                0                  3
[1] 2 2
[1] FALSE
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    18   0
  21Q GAIN WILD-TYPE 248   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     18    0
  21Q GAIN WILD-TYPE  248    4
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               18                248
  1                0                  4
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     9  17
  21Q GAIN WILD-TYPE 109 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9   17
  21Q GAIN WILD-TYPE  109  235
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                9                109
  MALE                 17                235
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    24   0
  21Q GAIN WILD-TYPE 314   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     24    0
  21Q GAIN WILD-TYPE  314    9
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                24                314
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  21Q GAIN MUTATED                         0                       25
  21Q GAIN WILD-TYPE                       3                      335
                    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                  3
  HEPATOCELLULAR CARCINOMA                       25                335
  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 305  15   1  16
D38V10, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               19                305
  R1                2                 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
  21Q GAIN MUTATED                                  0     8
  21Q GAIN WILD-TYPE                                2   150
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           2    15
  21Q GAIN WILD-TYPE                        15   168
D38V11, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           8                150
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          15                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"
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  24
  21Q GAIN WILD-TYPE  15 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   24
  21Q GAIN WILD-TYPE   15  311
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               24                311
[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 207 110
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                47                317 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                110 
$`22Q GAIN MUTATED`
TCGA-BC-A112 TCGA-DD-A4ND TCGA-ES-A2HS TCGA-G3-A3CG TCGA-2Y-A9GU TCGA-2Y-A9GY 
        5.03        90.28        22.62        22.13        63.75        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-BC-A10R TCGA-BC-A69H 
       27.88        56.91         1.18        13.02        10.13        14.60 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UE 
        0.66         4.24         3.19        10.36        11.41         8.94 
TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A9FW TCGA-DD-A118 TCGA-DD-A11D 
        9.83        12.56         9.14         8.15       113.00        51.29 
TCGA-DD-A1EJ TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACJ TCGA-DD-AAE0 TCGA-DD-AAED 
       33.04       114.35        76.41        69.11        18.25        25.08 
TCGA-DD-AAEK TCGA-DD-AAVY TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O6 
       35.08        64.77        13.35         0.20        13.41         1.84 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-G3-A25X TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-UB-A7MA 
       19.10        27.88        58.49        20.78        11.80        27.88 
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-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        26.83        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       18.90        23.64         9.96         8.12         6.38        81.73 
TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       30.74        22.06         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       12.72        24.56         0.76         7.04        10.32        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX 
        0.69        40.80        23.80        53.39        41.79        80.28 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
      120.82        40.41        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
       22.92         8.55        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO 
       44.42        45.93         0.26        22.36        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
       44.81        13.45         2.86         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IE 
        3.32         9.86         9.96        11.93         9.99         7.13 
TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU 
       21.34        12.00        13.12         8.61         4.60        11.31 
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-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        21.76        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       49.15         6.02        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-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-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        35.67        13.48         0.53        11.41        75.65 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       53.19         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-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-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       19.30        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
        4.64        23.74        15.72        26.63        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        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        60.99 
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-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       14.40        60.89        23.97        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
       22.95        20.42        17.10        14.70        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        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        15.52        36.10        19.76        16.44 
TCGA-UB-A7MD TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
        1.71        11.34        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       33.86        30.41        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       35.87        25.15        12.99        45.57        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     161       70         3         50          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q GAIN MUTATED            2        0         0         0
  22Q GAIN WILD-TYPE          5        2         1         2
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  12                161
  STAGE II                 17                 70
  STAGE III                 0                  3
  STAGE IIIA               12                 50
  STAGE IIIB                2                  7
  STAGE IIIC                2                  5
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED    13  17  16   2
  22Q GAIN WILD-TYPE 170  78  61  10
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               13                170
  T2               17                 78
  T3               16                 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"
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    30   1
  22Q GAIN WILD-TYPE 224   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     30    1
  22Q GAIN WILD-TYPE  224    2
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               30                224
  1                1                  2
[1] 2 2
[1] FALSE
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    33   0
  22Q GAIN WILD-TYPE 233   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     33    0
  22Q GAIN WILD-TYPE  233    4
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               33                233
  1                0                  4
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    19  29
  22Q GAIN WILD-TYPE  99 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     19   29
  22Q GAIN WILD-TYPE   99  223
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               19                 99
  MALE                 29                223
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    46   0
  22Q GAIN WILD-TYPE 292   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     46    0
  22Q GAIN WILD-TYPE  292    9
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                46                292
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  22Q GAIN MUTATED                         0                       46
  22Q GAIN WILD-TYPE                       3                      314
                    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                  3
  HEPATOCELLULAR CARCINOMA                       46                314
  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 284  14   1  16
D39V10, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               40                284
  R1                3                 14
  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                                2   135
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           2    23
  22Q GAIN WILD-TYPE                        15   160
D39V11, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          23                135
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          23                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"
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  47
  22Q GAIN WILD-TYPE  15 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   47
  22Q GAIN WILD-TYPE   15  288
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               47                288
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    26  15
  XP GAIN WILD-TYPE 209 114
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               41               323 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               15               114 
$`XP GAIN MUTATED`
TCGA-EP-A3JL TCGA-G3-A3CG TCGA-LG-A6GG TCGA-2Y-A9H1 TCGA-BC-A10R TCGA-BC-A10U 
        9.96        22.13        12.72        40.41        10.13        27.52 
TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-A5UC TCGA-CC-A7IJ 
        1.12         0.26        12.72         2.86        11.41        12.56 
TCGA-CC-A8HU TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NK TCGA-DD-A73D TCGA-DD-A73G 
       11.31        17.59        13.78        39.78        22.78       114.35 
TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACT TCGA-DD-AAD2 TCGA-DD-AADU TCGA-DD-AAE3 
       12.53        69.11        51.35        21.63        18.21        18.61 
TCGA-DD-AAE9 TCGA-DD-AAVV TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-EP-A12J TCGA-EP-A2KA 
       23.74        80.71        64.77        60.99        18.74        20.61 
TCGA-FV-A4ZQ TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-AAV5 TCGA-O8-A75V 
        0.39        19.53        25.25        20.42        11.64        17.69 
TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-ZS-A9CD 
       15.98         0.99        18.28        30.41        45.57 

$`XP GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        81.73        30.74        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
        2.14        31.27        24.56         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU 
       29.52         0.69        40.80        23.80        53.39        63.75 
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 
       41.79        80.28        24.89        27.88       120.82        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       49.84        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55        13.02        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-A216 TCGA-BC-A217 
       27.52         2.99        25.32        23.38        44.42        45.93 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         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-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.86         9.96        10.36        11.93         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-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        9.14         4.60         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-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-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11        30.61        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.97        30.15        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-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-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF 
       11.41        75.65        76.41        55.40        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42         6.41        53.19         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
       42.81        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-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        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-AADW 
       14.89        15.06        14.33        66.67        15.58        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-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       90.48        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-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-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        13.68        51.06        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       58.49        14.86        21.53        25.64         5.92        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       22.95        17.10        14.70        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-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
        7.53        10.85        58.88        26.27        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
        1.71        10.75        11.34        12.99        20.22        24.85 
TCGA-XR-A8TD TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       33.86        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        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 
            18.61             19.99 
[1] "0.3 - 114.3 (18.6)" "0.0 - 120.8 (20.0)"
[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     155       76         3         55          8          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XP GAIN MUTATED          0         0         0
  XP GAIN WILD-TYPE        2         1         2
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 18               155
  STAGE II                11                76
  STAGE III                0                 3
  STAGE IIIA               7                55
  STAGE IIIB               1                 8
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP GAIN MUTATED    18  12  10   1
  XP GAIN WILD-TYPE 165  83  67  11
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              18               165
  T2              12                83
  T3              10                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"
D40V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    25   0
  XP GAIN WILD-TYPE 229   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     25    0
  XP GAIN WILD-TYPE  229    3
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              25               229
  1               0                 3
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    28   0
  XP GAIN WILD-TYPE 238   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     28    0
  XP GAIN WILD-TYPE  238    4
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              28               238
  1               0                 4
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    13  28
  XP GAIN WILD-TYPE 105 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     13   28
  XP GAIN WILD-TYPE  105  224
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              13               105
  MALE                28               224
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    36   2
  XP GAIN WILD-TYPE 302   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     36    2
  XP GAIN WILD-TYPE  302    7
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               36               302
  YES               2                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XP GAIN MUTATED                         0                       41
  XP GAIN WILD-TYPE                       3                      319
                   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                 3
  HEPATOCELLULAR CARCINOMA                      41               319
  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 288  14   1  20
D40V10, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              36               288
  R1               3                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
  XP GAIN MUTATED                                  1    17
  XP GAIN WILD-TYPE                                1   141
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                           1    20
  XP GAIN WILD-TYPE                        16   163
D40V11, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                         17               141
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         20               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"
D40V12, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     2  36
  XP GAIN WILD-TYPE  14 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2   36
  XP GAIN WILD-TYPE   14  299
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              36               299
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    42  18
  XQ GAIN WILD-TYPE 193 111
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               60               304 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               18               111 
$`XQ GAIN MUTATED`
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-G3-A3CG TCGA-LG-A6GG TCGA-2Y-A9GT TCGA-2Y-A9H1 
        9.96        22.62        22.13        12.72        53.39        40.41 
TCGA-2Y-A9H4 TCGA-5R-AA1C TCGA-BC-A10U TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A69I 
       47.74        17.10        27.52         1.12         0.26        12.72 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A5UC TCGA-CC-A7IH TCGA-CC-A7IJ 
        0.66         2.86         3.35        11.41        12.00        12.56 
TCGA-CC-A8HU TCGA-DD-A11A TCGA-DD-A39V TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NF 
       11.31         2.60        21.14        17.59        13.78        30.97 
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-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 
       90.48        89.69        80.71        64.77        65.39        60.99 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A3CJ TCGA-G3-A5SI 
       18.74        20.61         0.39        53.79        19.53        25.25 
TCGA-G3-A5SL TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-K7-A6G5 TCGA-MI-A75G TCGA-O8-A75V 
       20.42        13.55        11.64        16.83        22.95        17.69 
TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-ZS-A9CD TCGA-ZS-A9CG 
       15.98         0.99        18.28        30.41        45.57        11.21 

$`XQ GAIN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.17        21.83        18.90        23.64         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       81.73        30.74        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       31.27        24.56         0.76         7.04        10.32        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
        0.69        40.80        23.80        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 
       24.89        27.88       120.82        56.91        49.84        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        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-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO 
       23.38        44.42        45.93        22.36        14.60        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       44.81        13.45         4.24         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-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IK 
        8.94         7.13        21.34         9.83        13.12         8.61 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        9.14         4.60         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-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       33.04        18.35        13.64        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81         7.66        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NJ 
      107.11        30.61        33.14        32.52        30.15        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 
       71.80        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-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-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62         4.50        18.54        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-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-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
        4.64        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       35.08        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       62.47        66.25        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-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       19.99        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        28.27        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M5 
       25.64         5.92        19.23        22.95        17.10        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-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       12.23         0.89         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.20         2.99        37.71        17.06        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       29.79        13.97        12.03         9.57        16.67        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
        7.53        10.85        58.88        26.27        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
        1.71        10.75        11.34        12.99        20.22        24.85 
TCGA-XR-A8TD TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       33.86        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       35.87        25.15        12.99        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 
           19.135            19.890 
[1] "0.3 - 114.3 (19.1)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1.3"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ GAIN MUTATED        28       16         0         12          1          1
  XQ GAIN WILD-TYPE     145       71         3         50          8          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ GAIN MUTATED          0         0         0
  XQ GAIN WILD-TYPE        2         1         2
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 28               145
  STAGE II                16                71
  STAGE III                0                 3
  STAGE IIIA              12                50
  STAGE IIIB               1                 8
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED    28  17  14   1
  XQ GAIN WILD-TYPE 155  78  63  11
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              28               155
  T2              17                78
  T3              14                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"
D41V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    40   0
  XQ GAIN WILD-TYPE 214   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     40    0
  XQ GAIN WILD-TYPE  214    3
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              40               214
  1               0                 3
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    42   0
  XQ GAIN WILD-TYPE 224   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     42    0
  XQ GAIN WILD-TYPE  224    4
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              42               224
  1               0                 4
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    14  46
  XQ GAIN WILD-TYPE 104 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     14   46
  XQ GAIN WILD-TYPE  104  206
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              14               104
  MALE                46               206
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    52   3
  XQ GAIN WILD-TYPE 286   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     52    3
  XQ GAIN WILD-TYPE  286    6
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               52               286
  YES               3                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XQ GAIN MUTATED                         0                       60
  XQ GAIN WILD-TYPE                       3                      300
                   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                 3
  HEPATOCELLULAR CARCINOMA                      60               300
  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    52   3   0   4
  XQ GAIN WILD-TYPE 272  14   1  17
D41V10, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              52               272
  R1               3                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 GAIN MUTATED                                  1    24
  XQ GAIN WILD-TYPE                                1   134
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           4    29
  XQ GAIN WILD-TYPE                        13   154
D41V11, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                         24               134
  BLACK OR AFRICAN AMERICAN                      4                13
  WHITE                                         29               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"
D41V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     2  55
  XQ GAIN WILD-TYPE  14 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2   55
  XQ GAIN WILD-TYPE   14  280
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              55               280
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    50  27
  1P LOSS WILD-TYPE 185 102
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               77               287 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               27               102 
$`1P LOSS MUTATED`
TCGA-2Y-A9H6 TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-ZP-A9D1 TCGA-2Y-A9GY TCGA-2Y-A9H3 
       11.74        22.62        81.73         0.69        24.89        49.84 
TCGA-2Y-A9H5 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10S TCGA-BC-A217 
       18.25        13.02        10.78        10.59        46.78        45.93 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD 
       14.60         4.24         3.19        10.36        11.93         9.99 
TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 
       12.56         9.14         9.17         8.15        79.73       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A3A1 
        7.33         0.46        90.71        49.15        33.04         7.66 
TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACJ 
       30.61        30.15        29.56         9.30         0.53        69.11 
TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD1 TCGA-DD-AADA 
       42.81        13.64        51.52        46.82        18.54        40.54 
TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       35.05        14.89        19.30        18.25        18.25        18.15 
TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVZ TCGA-ED-A66X 
       18.61        35.08        89.69        59.93        62.47        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        9.73        12.82        13.41        13.35         1.84         0.20 
TCGA-EP-A2KC TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X 
        0.62        27.88         0.33        13.68        53.79        58.49 
TCGA-G3-A25Y TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-AAV6 TCGA-KR-A7K2 
       14.86        20.42        17.10        14.70         2.14        27.25 
TCGA-LG-A9QC TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       13.97        15.52        36.10         0.99        12.99 

$`1P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        38.40         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64         9.96         8.12         6.38 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       30.74        22.13        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       31.27        12.72        24.56         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       29.52        40.80        23.80        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 
       80.28        27.88       120.82        40.41        56.91        47.74 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-AAPD TCGA-5R-AA1C 
       20.81        22.92         1.18         8.55         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-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-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-BW-A5NO TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
       13.45         0.66         2.86         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE 
        3.32         9.86         9.96        11.41         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT 
       21.34         9.83        12.00        13.12         8.61         4.60 
TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A 
       11.31         6.94        37.78        83.57        53.33         2.60 
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-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       11.47        12.95        45.11         6.02        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-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        32.52        30.97        30.51        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       23.93        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
       13.48        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-AACK 
       71.80        12.00        15.42         6.41        53.19         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
        3.52        58.16        61.68        14.20        59.31        51.35 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 
       50.33         5.59        47.67         5.62         4.50        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       42.58        44.22        22.09        40.08        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-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-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       15.58        18.21        20.98        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       15.72        25.08        26.63        25.78        50.33        90.48 
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-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       28.08        13.91         0.20         0.20        14.04        13.15 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61        19.59        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       60.89        23.97        19.10        12.03         0.03         0.39 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       51.06        28.27        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       19.23        25.25        22.95        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-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       11.64        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QD 
       37.71        17.06        16.83        11.80        29.79        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       11.34        20.22        24.85        18.28        33.86        30.41 
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-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        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 
            15.52             20.78 
[1] "0.2 - 113.0 (15.5)" "0.0 - 120.8 (20.8)"
[1] "hr=" "1"  
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P LOSS MUTATED        33       20         1         15          2          1
  1P LOSS WILD-TYPE     140       67         2         47          7          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P LOSS MUTATED          2         0         1
  1P LOSS WILD-TYPE        0         1         1
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 33               140
  STAGE II                20                67
  STAGE III                1                 2
  STAGE IIIA              15                47
  STAGE IIIB               2                 7
  STAGE IIIC               1                 6
  STAGE IV                 2                 0
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED    35  21  21   1
  1P LOSS WILD-TYPE 148  74  56  11
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              35               148
  T2              21                74
  T3              21                56
  T4               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    57   1
  1P LOSS WILD-TYPE 197   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     57    1
  1P LOSS WILD-TYPE  197    2
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              57               197
  1               1                 2
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    65   3
  1P LOSS WILD-TYPE 201   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     65    3
  1P LOSS WILD-TYPE  201    1
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              65               201
  1               3                 1
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    30  48
  1P LOSS WILD-TYPE  88 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     30   48
  1P LOSS WILD-TYPE   88  204
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              30                88
  MALE                48               204
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    74   0
  1P LOSS WILD-TYPE 264   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     74    0
  1P LOSS WILD-TYPE  264    9
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               74               264
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1P LOSS MUTATED                         0                       75
  1P LOSS WILD-TYPE                       3                      285
                   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                 3
  HEPATOCELLULAR CARCINOMA                      75               285
  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    69   3   1   5
  1P LOSS WILD-TYPE 255  14   0  16
D42V10, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              69               255
  R1               3                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
  1P LOSS MUTATED                                  0    41
  1P LOSS WILD-TYPE                                2   117
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           3    33
  1P LOSS WILD-TYPE                        14   150
D42V11, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         41               117
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         33               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"
D42V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3  72
  1P LOSS WILD-TYPE  13 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3   72
  1P LOSS WILD-TYPE   13  263
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              72               263
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    10  10
  1Q LOSS WILD-TYPE 225 119
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               344 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               119 
$`1Q LOSS MUTATED`
TCGA-ES-A2HS TCGA-2Y-A9GY TCGA-2Y-A9H5 TCGA-BC-A10S TCGA-BC-A217 TCGA-CC-5258 
       22.62        24.89        18.25        46.78        45.93         4.24 
TCGA-CC-A7IJ TCGA-DD-A11B TCGA-DD-A1EJ TCGA-DD-A3A1 TCGA-DD-AACW TCGA-DD-AADW 
       12.56         0.46        33.04         7.66        46.82        19.30 
TCGA-DD-AAEK TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-FV-A496 TCGA-G3-A25U 
       35.08        13.41        13.35         0.20         0.33        53.79 
TCGA-G3-A25Y TCGA-UB-AA0U 
       14.86        10.75 

$`1Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        63.75        41.79        80.28        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       40.41        56.91        49.84        47.74        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        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-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-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
        1.12        44.42         0.26        22.36        14.60        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-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-A7IK TCGA-CC-A7IL 
       21.34         9.83        12.00        13.12         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-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-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-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-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        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        71.80        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-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-AADY 
       15.06        14.33        66.67        15.58        18.21        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        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 
       60.99        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-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.15         1.84        18.74        19.99        20.61        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-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       27.88        12.03         0.03         0.39        13.68        51.06 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        58.49        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-A7M5 
       19.23        25.25        22.95        20.42        17.10        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        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.20              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            53.79            120.82 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           16.555            19.990 
[1] "0.2 - 53.8 (16.6)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.8"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q LOSS MUTATED         8        6         0          4          0          1
  1Q LOSS WILD-TYPE     165       81         3         58          9          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q LOSS MUTATED          0         0         0
  1Q LOSS WILD-TYPE        2         1         2
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  8               165
  STAGE II                 6                81
  STAGE III                0                 3
  STAGE IIIA               4                58
  STAGE IIIB               0                 9
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED     9   6   5   0
  1Q LOSS WILD-TYPE 174  89  72  12
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               9               174
  T2               6                89
  T3               5                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"
D43V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    13   1
  1Q LOSS WILD-TYPE 241   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     13    1
  1Q LOSS WILD-TYPE  241    2
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              13               241
  1               1                 2
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    15   0
  1Q LOSS WILD-TYPE 251   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     15    0
  1Q LOSS WILD-TYPE  251    4
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              15               251
  1               0                 4
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9  11
  1Q LOSS WILD-TYPE 109 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9   11
  1Q LOSS WILD-TYPE  109  241
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               9               109
  MALE                11               241
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    18   0
  1Q LOSS WILD-TYPE 320   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     18    0
  1Q LOSS WILD-TYPE  320    9
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               18               320
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1Q LOSS MUTATED                         0                       19
  1Q LOSS WILD-TYPE                       3                      341
                   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                 3
  HEPATOCELLULAR CARCINOMA                      19               341
  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    17   1   0   2
  1Q LOSS WILD-TYPE 307  16   1  19
D43V10, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              17               307
  R1               1                16
  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    10
  1Q LOSS WILD-TYPE                                2   148
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           0     9
  1Q LOSS WILD-TYPE                        17   174
D43V11, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         10               148
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                          9               174
[1] 4 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  18
  1Q LOSS WILD-TYPE  16 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   18
  1Q LOSS WILD-TYPE   16  317
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              18               317
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    23   8
  2P LOSS WILD-TYPE 212 121
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               31               333 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8               121 
$`2P LOSS MUTATED`
TCGA-FV-A3I1 TCGA-T1-A6J8 TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Y 
        8.12         0.76        20.81        13.02        10.78        23.38 
TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A3EP TCGA-CC-A7II TCGA-CC-A7IL TCGA-DD-A11C 
        0.26        14.60        13.45        13.12         9.14        21.76 
TCGA-DD-A39Y TCGA-DD-AACE TCGA-DD-AACU TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADN 
        5.62        71.80        51.52        35.67        20.91        29.52 
TCGA-DD-AADW TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-G3-A25S 
       19.30        29.92         9.73         0.20         0.20        13.68 
TCGA-G3-A5SM TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A6M5 TCGA-RC-A7SH 
       17.10        11.87         2.20        27.25         0.49        15.39 
TCGA-WQ-AB4B 
       12.99 

$`2P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF 
       20.75         2.14        31.27        12.72        24.56         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       10.32        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       63.75        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H9 
       40.41        56.91        49.84        47.74        18.25        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        1.18         8.55        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-A216 
       27.52        27.52         2.99        25.32         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO 
       45.93        22.36        12.72        18.48        44.81         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-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-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-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        55.69        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-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-AACG 
       75.65        76.41        55.40        12.53        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        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-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-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       37.64        35.05        34.49         0.39        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 
       14.33        66.67        15.58        18.21        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-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        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 
       60.99        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-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
       12.03         0.03         0.33         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M5 
       19.53        19.23        25.25        22.95        20.42        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-GJ-A3OU 
       12.23        13.55         0.89        11.64         2.14        28.90 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
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-A6M4 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
       21.01         3.09         0.72         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 
        1.71        15.98        10.75        11.34         0.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        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 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.20              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            71.80            120.82 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            13.45             20.42 
[1] "0.2 - 71.8 (13.4)"  "0.0 - 120.8 (20.4)"
[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     159       76         3         59          8          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P LOSS MUTATED          0         1         0
  2P LOSS WILD-TYPE        2         0         2
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 14               159
  STAGE II                11                76
  STAGE III                0                 3
  STAGE IIIA               3                59
  STAGE IIIB               1                 8
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  STAGE IVA                1                 0
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED    17  11   4   1
  2P LOSS WILD-TYPE 166  84  73  11
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1              17               166
  T2              11                84
  T3               4                73
  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    19   1
  2P LOSS WILD-TYPE 235   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     19    1
  2P LOSS WILD-TYPE  235    2
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              19               235
  1               1                 2
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    26   0
  2P LOSS WILD-TYPE 240   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     26    0
  2P LOSS WILD-TYPE  240    4
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              26               240
  1               0                 4
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     8  25
  2P LOSS WILD-TYPE 110 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      8   25
  2P LOSS WILD-TYPE  110  227
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               8               110
  MALE                25               227
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    27   1
  2P LOSS WILD-TYPE 311   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     27    1
  2P LOSS WILD-TYPE  311    8
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               27               311
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2P LOSS MUTATED                         1                       31
  2P LOSS WILD-TYPE                       2                      329
                   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                        1                 2
  HEPATOCELLULAR CARCINOMA                      31               329
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    28   1   0   4
  2P LOSS WILD-TYPE 296  16   1  17
D44V10, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              28               296
  R1               1                16
  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                                  1    15
  2P LOSS WILD-TYPE                                1   143
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           2    15
  2P LOSS WILD-TYPE                        15   168
D44V11, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                         15               143
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         15               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"
D44V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  29
  2P LOSS WILD-TYPE  16 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   29
  2P LOSS WILD-TYPE   16  306
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              29               306
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    26  10
  2Q LOSS WILD-TYPE 209 119
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               36               328 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               119 
$`2Q LOSS MUTATED`
TCGA-FV-A3I1 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-2Y-A9GU TCGA-3K-AAZ8 TCGA-5C-A9VG 
        8.12         0.76         7.04        63.75        13.02        10.78 
TCGA-BC-A10Y TCGA-BC-A3KF TCGA-BD-A3EP TCGA-CC-5264 TCGA-CC-A7II TCGA-CC-A7IL 
       23.38         0.26        13.45         3.35        13.12         9.14 
TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A39Y TCGA-DD-A4NJ TCGA-DD-A73B TCGA-DD-AACE 
       83.57        21.76         5.62        30.51         9.30        71.80 
TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE6 
       35.67        20.91        29.52        19.30        20.98         4.64 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-G3-A5SM 
       29.92         9.73         0.20         0.20        14.04        17.10 
TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A6M5 TCGA-RC-A7SH TCGA-WQ-AB4B 
       11.87         2.20        27.25         0.49        15.39        12.99 

$`2Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V 
       20.75         2.14        31.27        12.72        24.56        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GW 
       29.52         0.69        40.80        23.80        53.39        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       80.28        24.89        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       49.84        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
        8.55        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-A10Z TCGA-BC-A216 TCGA-BC-A217 
       27.52         2.99        25.32         1.12        44.42        45.93 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO 
       22.36        14.60        12.72        18.48        44.81         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        4.24         2.86         3.19         3.39         4.24         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-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ 
        8.94         7.13        21.34         9.83        12.00        12.56 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        8.61         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.97        30.15        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52         3.78        37.64        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.21        18.25        18.25        18.15        18.61        19.99 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        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        60.99        53.69        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       13.35        12.82        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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
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-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-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
       28.90         1.02         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       11.80        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M6 TCGA-RC-A7S9 
       17.69        21.01         3.09         0.72         0.30        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        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       12.99        45.57        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 
           13.070            20.515 
[1] "0.2 - 83.6 (13.1)"  "0.0 - 120.8 (20.5)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q LOSS MUTATED        16       11         0          7          1          0
  2Q LOSS WILD-TYPE     157       76         3         55          8          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q LOSS MUTATED          0         1         0
  2Q LOSS WILD-TYPE        2         0         2
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 16               157
  STAGE II                11                76
  STAGE III                0                 3
  STAGE IIIA               7                55
  STAGE IIIB               1                 8
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  STAGE IVA                1                 0
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED    18  11   8   1
  2Q LOSS WILD-TYPE 165  84  69  11
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1              18               165
  T2              11                84
  T3               8                69
  T4               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    24   1
  2Q LOSS WILD-TYPE 230   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     24    1
  2Q LOSS WILD-TYPE  230    2
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              24               230
  1               1                 2
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    30   0
  2Q LOSS WILD-TYPE 236   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     30    0
  2Q LOSS WILD-TYPE  236    4
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              30               236
  1               0                 4
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    11  27
  2Q LOSS WILD-TYPE 107 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11   27
  2Q LOSS WILD-TYPE  107  225
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              11               107
  MALE                27               225
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    32   1
  2Q LOSS WILD-TYPE 306   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     32    1
  2Q LOSS WILD-TYPE  306    8
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               32               306
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2Q LOSS MUTATED                         1                       36
  2Q LOSS WILD-TYPE                       2                      324
                   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                        1                 2
  HEPATOCELLULAR CARCINOMA                      36               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
  2Q LOSS MUTATED    33   0   0   5
  2Q LOSS WILD-TYPE 291  17   1  16
D45V10, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              33               291
  R1               0                17
  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                                  1    18
  2Q LOSS WILD-TYPE                                1   140
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           2    17
  2Q LOSS WILD-TYPE                        15   166
D45V11, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                         18               140
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         17               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"
D45V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1  32
  2Q LOSS WILD-TYPE  15 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   32
  2Q LOSS WILD-TYPE   15  303
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              32               303
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    35  16
  3P LOSS WILD-TYPE 200 113
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               51               313 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               16               113 
$`3P LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A4NI TCGA-KR-A7K7 TCGA-UB-A7MF TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        5.03        26.83        31.27         7.04         0.69        40.80 
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-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UE 
        0.66        10.13         4.24         9.96        10.36         8.94 
TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1E9 
        7.13        13.12         8.15        79.73       113.00        90.71 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-AACO TCGA-DD-AADO TCGA-DD-AADY 
       30.61        33.14        73.81        61.68        14.89        18.25 
TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E 
       89.69        72.39         9.73         0.20         0.20        13.41 
TCGA-ED-A97K TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A7M5 TCGA-G3-AAV1 
        0.20        27.88        51.06        58.49        14.70        11.80 
TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-MR-A8JO TCGA-RC-A6M4 TCGA-RC-A6M5 
        2.14        27.25        13.97        10.85         0.72         0.49 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-WQ-AB4B 
       16.44         1.71        12.99 

$`3P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       18.90        23.64         9.96        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TG 
        2.14        12.72        24.56         0.76        10.32        29.52 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       23.80        53.39        63.75        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
      120.82        40.41        47.74        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55        10.59        17.10        14.76         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        14.60        12.72        18.48        44.81        13.45 
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-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF 
        3.32         9.86        11.93        11.41         9.99        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
        9.83        12.00        12.56         8.61         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
       11.31         9.17         6.94        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
        7.33         2.60         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-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        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       35.08        90.48        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        60.99 
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-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J 
       12.82        14.04        13.15        13.35         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       60.89        23.97        19.10        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39        13.68        53.79        28.27        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-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       20.42        17.10        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        11.64        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       16.83        11.80        29.79        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       22.95        20.71         7.53        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       21.01         3.09         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME 
       15.39        15.52        36.10        27.88        19.76        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.75        11.34         0.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        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 

  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 
            13.41             20.61 
[1] "0.2 - 113.0 (13.4)" "0.0 - 120.8 (20.6)"
[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         15          2          2
  3P LOSS WILD-TYPE     160       72         3         47          7          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P LOSS MUTATED          0         1         1
  3P LOSS WILD-TYPE        2         0         1
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 13               160
  STAGE II                15                72
  STAGE III                0                 3
  STAGE IIIA              15                47
  STAGE IIIB               2                 7
  STAGE IIIC               2                 5
  STAGE IV                 0                 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                 T1  T2  T3  T4
  3P LOSS MUTATED    15  16  18   3
  3P LOSS WILD-TYPE 168  79  59   9
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              15               168
  T2              16                79
  T3              18                59
  T4               3                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    34   2
  3P LOSS WILD-TYPE 220   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     34    2
  3P LOSS WILD-TYPE  220    1
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              34               220
  1               2                 1
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    36   1
  3P LOSS WILD-TYPE 230   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     36    1
  3P LOSS WILD-TYPE  230    3
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              36               230
  1               1                 3
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    21  31
  3P LOSS WILD-TYPE  97 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     21   31
  3P LOSS WILD-TYPE   97  221
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              21                97
  MALE                31               221
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    48   0
  3P LOSS WILD-TYPE 290   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     48    0
  3P LOSS WILD-TYPE  290    9
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               48               290
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3P LOSS MUTATED                         2                       46
  3P LOSS WILD-TYPE                       1                      314
                   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                        2                 1
  HEPATOCELLULAR CARCINOMA                      46               314
  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    48   1   0   3
  3P LOSS WILD-TYPE 276  16   1  18
D46V10, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              48               276
  R1               1                16
  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                                2   136
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           2    28
  3P LOSS WILD-TYPE                        15   155
D46V11, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         22               136
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         28               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  47
  3P LOSS WILD-TYPE  15 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   47
  3P LOSS WILD-TYPE   15  288
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              47               288
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    29  11
  3Q LOSS WILD-TYPE 206 118
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               40               324 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               11               118 
$`3Q LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A4NI TCGA-KR-A7K7 TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GY 
        5.03        26.83        31.27         0.69        40.80        24.89 
TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-CC-5263 TCGA-CC-A5UE 
       49.84        18.25        13.02        10.78         4.24         8.94 
TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1E9 
        7.13        13.12         8.15        79.73       113.00        90.71 
TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-AACO TCGA-DD-AADO TCGA-DD-AADY TCGA-DD-AAVQ 
       33.14        73.81        61.68        14.89        18.25        89.69 
TCGA-DD-AAVU TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K 
       72.39         9.73         0.20        13.41         1.84         0.20 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-MR-A8JO 
       14.70        11.80         2.14        27.25        13.97        10.85 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-UB-A7MC TCGA-WQ-AB4B 
        0.72         0.49        16.44        12.99 

$`3Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       18.90        23.64         9.96        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
        2.14        12.72        24.56         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       29.52        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H8 
       27.88       120.82        40.41        56.91        47.74        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
       22.92         1.18         8.55        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       12.72        18.48        44.81        13.45         0.66         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-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF 
        9.96        10.36        11.93        11.41         9.99        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
        9.83        12.00        12.56         8.61         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
       11.31         9.17         6.94        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
        7.33         2.60         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.61        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        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        71.80        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-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-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-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       29.52        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       19.30        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV 
       50.33        35.08        90.48        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-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
       13.35         0.20        12.82        14.04        13.15        13.35 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        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-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
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-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       13.55         0.89        11.64        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       29.79        12.03         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-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       36.10        27.88        19.76         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
       11.34         0.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        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 
           13.690            20.515 
[1] "0.2 - 113.0 (13.7)" "0.0 - 120.8 (20.5)"
[1] "hr=" "1.3"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q LOSS MUTATED        11       11         0         12          2          2
  3Q LOSS WILD-TYPE     162       76         3         50          7          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q LOSS MUTATED          0         1         0
  3Q LOSS WILD-TYPE        2         0         2
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 11               162
  STAGE II                11                76
  STAGE III                0                 3
  STAGE IIIA              12                50
  STAGE IIIB               2                 7
  STAGE IIIC               2                 5
  STAGE IV                 0                 2
  STAGE IVA                1                 0
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED    13  12  14   2
  3Q LOSS WILD-TYPE 170  83  63  10
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              13               170
  T2              12                83
  T3              14                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"
D47V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    27   2
  3Q LOSS WILD-TYPE 227   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     27    2
  3Q LOSS WILD-TYPE  227    1
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              27               227
  1               2                 1
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    30   0
  3Q LOSS WILD-TYPE 236   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     30    0
  3Q LOSS WILD-TYPE  236    4
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              30               236
  1               0                 4
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    16  25
  3Q LOSS WILD-TYPE 102 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     16   25
  3Q LOSS WILD-TYPE  102  227
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              16               102
  MALE                25               227
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    38   0
  3Q LOSS WILD-TYPE 300   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     38    0
  3Q LOSS WILD-TYPE  300    9
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               38               300
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3Q LOSS MUTATED                         2                       37
  3Q LOSS WILD-TYPE                       1                      323
                   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                        2                 1
  HEPATOCELLULAR CARCINOMA                      37               323
  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    37   1   0   3
  3Q LOSS WILD-TYPE 287  16   1  18
D47V10, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              37               287
  R1               1                16
  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
  3Q LOSS MUTATED                                  0    18
  3Q LOSS WILD-TYPE                                2   140
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           1    22
  3Q LOSS WILD-TYPE                        16   161
D47V11, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         18               140
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         22               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"
D47V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  36
  3Q LOSS WILD-TYPE  15 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   36
  3Q LOSS WILD-TYPE   15  299
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              36               299
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    64  37
  4P LOSS WILD-TYPE 171  92
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              101               263 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               37                92 
$`4P LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEA 
        5.03        17.98        26.83        18.87        21.83        18.90 
TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-UB-A7MF TCGA-ZS-A9CE TCGA-2Y-A9GS 
       81.73         1.84        31.27         7.04        40.80        23.80 
TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Y 
       24.89        49.84        13.02        10.78         0.66        23.38 
TCGA-BC-A217 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A3MC 
       45.93        14.60        13.45         0.66         3.35        11.93 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        7.13        21.34        13.12        12.56         8.61         9.14 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 
        9.17         6.94         8.15        79.73        37.78         7.33 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 
        6.02        33.04        13.64        55.69         5.62        30.61 
TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACF 
       30.51        29.56         0.53        76.41        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACY TCGA-DD-AAD5 
       15.42        42.81        13.64        51.52        47.67        44.22 
TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADR TCGA-DD-AAE0 
       40.08        13.97        40.47        20.91        66.67        18.25 
TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       25.08        35.08        89.69        72.39        80.71        76.18 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 
       29.92        13.35        12.82         0.20        14.04         1.84 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U 
       19.59         0.62        23.97         0.33        13.68        53.79 
TCGA-G3-A25X TCGA-G3-A7M5 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 
       58.49        14.70        15.78        11.80         0.89         2.14 
TCGA-GJ-A3OU TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-MI-A75G TCGA-RC-A7SB 
       28.90        17.06        27.25        13.97        22.95        19.33 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-WQ-AB4B 
       15.52        36.10        19.76        16.44        15.98        12.99 
TCGA-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CF 
       20.22        22.78        13.55        25.15        79.30 

$`4P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
        0.36        90.28        21.17        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
        8.12         6.38        30.74        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TG 
        2.14        12.72        24.56         0.76        10.32        29.52 
TCGA-ZP-A9D1 TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
        0.69        53.39        63.75        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
      120.82        40.41        56.91        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D 
       22.92         1.18         8.55        10.59        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-A216 
       27.52        27.52         2.99        25.32         1.12        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5258 
        0.26        22.36        12.72        18.48        44.81         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-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IG 
        9.96        10.36        11.41         9.99         8.94         9.83 
TCGA-CC-A7IH TCGA-CC-A8HT TCGA-CC-A8HU TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
       12.00         4.60        11.31        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-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 
       49.15        18.35        21.14        27.19        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK 
       13.78        33.14        32.52        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-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       23.74        15.72        26.63        25.78        50.33        90.48 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       82.62        59.93        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        60.99        53.69        26.93        28.08        13.91 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
        9.73         0.20        13.15        13.41        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       18.74        19.99        20.61        11.93        14.40        60.89 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
       19.10        27.88        12.03         0.03         0.39        51.06 
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-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-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 
       11.87        14.14        15.65        12.23        13.55        11.64 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 
       11.87         1.02         2.20         2.99        37.71        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       11.80        29.79        12.03         9.57        16.67        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SF 
        3.09         0.72         0.49         0.30        21.04        19.04 
TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.39        27.88         1.71        10.75        11.34         0.99 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9CY 
       24.85        18.28        33.86        30.41        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.21        35.87        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 
            18.87             20.42 
[1] "0.2 - 89.7 (18.9)"  "0.0 - 120.8 (20.4)"
[1] "hr=" "1.2"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P LOSS MUTATED        43       31         0         20          2          2
  4P LOSS WILD-TYPE     130       56         3         42          7          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P LOSS MUTATED          2         0         1
  4P LOSS WILD-TYPE        0         1         1
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 43               130
  STAGE II                31                56
  STAGE III                0                 3
  STAGE IIIA              20                42
  STAGE IIIB               2                 7
  STAGE IIIC               2                 5
  STAGE IV                 2                 0
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P LOSS MUTATED    44  34  24   3
  4P LOSS WILD-TYPE 139  61  53   9
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              44               139
  T2              34                61
  T3              24                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"
D48V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    69   1
  4P LOSS WILD-TYPE 185   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     69    1
  4P LOSS WILD-TYPE  185    2
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              69               185
  1               1                 2
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    77   3
  4P LOSS WILD-TYPE 189   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     77    3
  4P LOSS WILD-TYPE  189    1
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              77               189
  1               3                 1
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    25  80
  4P LOSS WILD-TYPE  93 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     25   80
  4P LOSS WILD-TYPE   93  172
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              25                93
  MALE                80               172
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    96   2
  4P LOSS WILD-TYPE 242   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     96    2
  4P LOSS WILD-TYPE  242    7
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               96               242
  YES               2                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4P LOSS MUTATED                         0                      103
  4P LOSS WILD-TYPE                       3                      257
                   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                 3
  HEPATOCELLULAR CARCINOMA                     103               257
  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 230  14   0  14
D48V10, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              94               230
  R1               3                14
  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                                  1    54
  4P LOSS WILD-TYPE                                1   104
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           8    41
  4P LOSS WILD-TYPE                         9   142
D48V11, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                         54               104
  BLACK OR AFRICAN AMERICAN                      8                 9
  WHITE                                         41               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"
D48V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     7  94
  4P LOSS WILD-TYPE   9 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      7   94
  4P LOSS WILD-TYPE    9  241
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                 9
  NOT HISPANIC OR LATINO              94               241
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    89  53
  4Q LOSS WILD-TYPE 146  76
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              142               222 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               53                76 
$`4Q LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEA 
        5.03        17.98        26.83        18.87        21.83        18.90 
TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-T1-A6J8 
        8.12        81.73         1.84        31.27        12.72         0.76 
TCGA-UB-A7MF TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H2 
        7.04        29.52        40.80        23.80        24.89        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       49.84        20.81         1.18        13.02        10.78        10.59 
TCGA-5C-AAPD TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H 
        0.66        27.52        23.38        45.93         0.26        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-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B 
       30.61        30.15        30.51        29.56        73.81         9.30 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
        0.53        76.41        55.40        71.80        12.00        15.42 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU 
        3.52        58.16        42.81        13.64        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB 
       50.33        46.82         5.62        44.22        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP 
       13.97        40.47        35.67        20.91        14.89        15.06 
TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAED 
       66.67        18.25        18.25        18.15         4.64        25.08 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       35.08        89.69        59.93        72.39        80.71        76.18 
TCGA-DD-AAW0 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       66.25        13.35        12.82         0.20        14.04        13.15 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-G3-A25S 
       13.35         0.20        19.59         0.62        23.97        13.68 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M5 
       58.49        14.86        21.53        25.25        17.10        14.70 
TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-K7-A5RG 
       11.80         0.89         2.14        11.87        28.90        17.06 
TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-MI-A75G TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK 
       27.25        13.97        22.95        19.33        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       36.10        19.76        16.44        15.98         0.99        12.99 
TCGA-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D2 
       20.22        22.78        13.55        25.15 

$`4Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
        0.36        90.28        21.17        23.64         9.96        22.62 
TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 
        6.38        30.74        22.13        22.06        20.75         2.14 
TCGA-MI-A75H TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       24.56        10.32         0.69        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       80.28        27.88       120.82        40.41        47.74        18.25 
TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       22.92         8.55        17.10        14.76         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO 
       25.32         1.12        44.42        22.36        12.72        18.48 
TCGA-BD-A2L6 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       44.81         4.24         2.86         3.19         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A8HT 
        3.32         9.96        11.41         9.83        12.00         4.60 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       83.57       113.00         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-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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       33.14        32.52        30.97        39.78        56.25       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       12.26         0.30        80.75        78.84        23.93        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 
       22.78         1.45        35.67       114.35        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       75.65        12.53         6.41        53.19        69.11         0.30 
TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       61.68        14.20        51.35         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADE 
       18.54        21.63        42.58        22.09        40.54        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN 
        3.78        37.64        35.05        34.49         0.39        29.52 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 
       14.33        15.58        18.21        19.30        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       19.99        23.74        15.72        26.63        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW1 
       90.48        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 
       60.99        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-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       20.61        11.93        14.40        60.89        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
       12.03         0.03         0.33         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       28.27        25.64         5.92        19.53        19.23        22.95 
TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.42        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       12.23        13.55        11.64         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C 
       37.71        16.83        11.80        29.79        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       16.67        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L 
       21.04        19.04        27.88         1.71        10.75        11.34 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9CY 
       24.85        18.28        33.86        30.41        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       23.21        35.87        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 
            17.54             20.88 
[1] "0.2 - 89.7 (17.5)"  "0.0 - 120.8 (20.9)"
[1] "hr=" "1.3"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED        64       38         1         26          4          2
  4Q LOSS WILD-TYPE     109       49         2         36          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q LOSS MUTATED          2         0         1
  4Q LOSS WILD-TYPE        0         1         1
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 64               109
  STAGE II                38                49
  STAGE III                1                 2
  STAGE IIIA              26                36
  STAGE IIIB               4                 5
  STAGE IIIC               2                 5
  STAGE IV                 2                 0
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q LOSS MUTATED    67  41  33   5
  4Q LOSS WILD-TYPE 116  54  44   7
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              67               116
  T2              41                54
  T3              33                44
  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   103   1
  4Q LOSS WILD-TYPE 151   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    103    1
  4Q LOSS WILD-TYPE  151    2
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             103               151
  1               1                 2
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   114   3
  4Q LOSS WILD-TYPE 152   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    114    3
  4Q LOSS WILD-TYPE  152    1
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             114               152
  1               3                 1
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    39 107
  4Q LOSS WILD-TYPE  79 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     39  107
  4Q LOSS WILD-TYPE   79  145
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              39                79
  MALE               107               145
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   134   3
  4Q LOSS WILD-TYPE 204   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    134    3
  4Q LOSS WILD-TYPE  204    6
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              134               204
  YES               3                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4Q LOSS MUTATED                         0                      143
  4Q LOSS WILD-TYPE                       3                      217
                   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                 3
  HEPATOCELLULAR CARCINOMA                     143               217
  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 191  13   0  13
D49V10, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             133               191
  R1               4                13
  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                                  1    80
  4Q LOSS WILD-TYPE                                1    78
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           9    56
  4Q LOSS WILD-TYPE                         8   127
D49V11, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                         80                78
  BLACK OR AFRICAN AMERICAN                      9                 8
  WHITE                                         56               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"
D49V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     8 133
  4Q LOSS WILD-TYPE   8 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8  133
  4Q LOSS WILD-TYPE    8  202
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                 8
  NOT HISPANIC OR LATINO             133               202
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    17  11
  5P LOSS WILD-TYPE 218 118
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28               336 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               118 
$`5P LOSS MUTATED`
TCGA-ES-A2HS TCGA-G3-A7M9 TCGA-5C-AAPD TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-A3M9 
       22.62         1.84         0.66        46.78         4.24         9.86 
TCGA-CC-A7IE TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HV TCGA-DD-A11A TCGA-DD-A1EH 
        7.13        12.56         8.61         9.17         2.60        49.15 
TCGA-DD-A1EJ TCGA-DD-A4NB TCGA-DD-AACS TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADG 
       33.04        32.52        59.31        40.83        40.47        37.64 
TCGA-DD-AADI TCGA-DD-AADW TCGA-DD-AAVQ TCGA-ED-A97K TCGA-FV-A496 TCGA-G3-A25S 
       35.67        19.30        89.69         0.20         0.33        13.68 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-UB-A7MB TCGA-WX-AA44 
        2.14        11.87        19.76        20.22 

$`5P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
        6.38        81.73        30.74        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       10.32        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       63.75        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       40.41        56.91        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 
       12.72        18.48        44.81        13.45         0.66         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-A7IF 
       10.36        11.93        11.41         9.99         8.94        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
        9.83        12.00        13.12         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-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-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-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        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        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU 
       42.81        61.68        13.64        14.20        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADK 
       40.54        13.97        39.52         3.78        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       66.67        15.58        18.21        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        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        90.48 
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        60.99        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-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-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
       27.88        12.03         0.03         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
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-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A3OU 
       11.80        12.23        13.55         0.89        11.64        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       36.10        27.88        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
       11.34         0.99        12.99        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        79.30        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 
            16.49             19.99 
[1] "0.2 - 89.7 (16.5)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.4"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P LOSS MUTATED        12        6         1          7          1          1
  5P LOSS WILD-TYPE     161       81         2         55          8          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P LOSS MUTATED          0         0         0
  5P LOSS WILD-TYPE        2         1         2
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 12               161
  STAGE II                 6                81
  STAGE III                1                 2
  STAGE IIIA               7                55
  STAGE IIIB               1                 8
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED    13   6  10   0
  5P LOSS WILD-TYPE 170  89  67  12
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              13               170
  T2               6                89
  T3              10                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"
D50V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    22   1
  5P LOSS WILD-TYPE 232   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     22    1
  5P LOSS WILD-TYPE  232    2
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              22               232
  1               1                 2
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    24   0
  5P LOSS WILD-TYPE 242   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     24    0
  5P LOSS WILD-TYPE  242    4
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              24               242
  1               0                 4
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     7  22
  5P LOSS WILD-TYPE 111 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      7   22
  5P LOSS WILD-TYPE  111  230
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               7               111
  MALE                22               230
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    24   1
  5P LOSS WILD-TYPE 314   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     24    1
  5P LOSS WILD-TYPE  314    8
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               24               314
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5P LOSS MUTATED                         1                       26
  5P LOSS WILD-TYPE                       2                      334
                   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                 2
  HEPATOCELLULAR CARCINOMA                      26               334
  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    26   1   0   2
  5P LOSS WILD-TYPE 298  16   1  19
D50V10, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              26               298
  R1               1                16
  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                                2   141
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           1    11
  5P LOSS WILD-TYPE                        16   172
D50V11, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         17               141
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         11               172
[1] 4 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  28
  5P LOSS WILD-TYPE  15 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   28
  5P LOSS WILD-TYPE   15  307
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              28               307
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    20  16
  5Q LOSS WILD-TYPE 215 113
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               36               328 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               16               113 
$`5Q LOSS MUTATED`
TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-UB-A7MF TCGA-5C-AAPD TCGA-BC-A10R 
       22.62        81.73         1.84         7.04         0.66        10.13 
TCGA-BC-A10S TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7II 
       46.78         4.24         9.86         9.99         7.13        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HV TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A1EH 
       12.56         8.61         9.17         2.60        12.95        49.15 
TCGA-DD-A1EJ TCGA-DD-A4NB TCGA-DD-AACS TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADD 
       33.04        32.52        59.31        40.08        40.83        40.47 
TCGA-DD-AADI TCGA-DD-AADW TCGA-DD-AAVQ TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A3I0 
       35.67        19.30        89.69         1.84         0.20        27.88 
TCGA-FV-A496 TCGA-G3-A7M6 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-UB-A7MB TCGA-WX-AA44 
        0.33        20.78         2.14        11.87        19.76        20.22 

$`5Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 
        6.38        30.74        22.13        22.06        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TG 
       31.27        12.72        24.56         0.76        10.32        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
        0.69        40.80        23.80        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       80.28        24.89        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       49.84        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55        13.02        10.78        10.59        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10U 
        1.51        48.99        27.91        37.32        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
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-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45         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-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        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        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU 
       42.81        61.68        13.64        14.20        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
       18.54        21.63        42.58        44.22        22.09        40.54 
TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK 
       13.97        39.52         3.78        37.64        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-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       66.67        15.58        18.21        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        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        90.48 
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        60.99        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-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-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 
       11.93        14.40        60.89        23.97        19.10        12.03 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.39        13.68        51.06        53.79        28.27 
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-A7M5 
       19.23        25.25        22.95        20.42        17.10        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        11.64        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       12.99        24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       12.99        45.57        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 
           13.035            20.055 
[1] "0.2 - 89.7 (13.0)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.6"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED        14        6         1         12          1          1
  5Q LOSS WILD-TYPE     159       81         2         50          8          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q LOSS MUTATED          0         0         0
  5Q LOSS WILD-TYPE        2         1         2
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 14               159
  STAGE II                 6                81
  STAGE III                1                 2
  STAGE IIIA              12                50
  STAGE IIIB               1                 8
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q LOSS MUTATED    15   6  16   0
  5Q LOSS WILD-TYPE 168  89  61  12
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              15               168
  T2               6                89
  T3              16                61
  T4               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    25   1
  5Q LOSS WILD-TYPE 229   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     25    1
  5Q LOSS WILD-TYPE  229    2
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              25               229
  1               1                 2
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    29   0
  5Q LOSS WILD-TYPE 237   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     29    0
  5Q LOSS WILD-TYPE  237    4
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              29               237
  1               0                 4
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    13  24
  5Q LOSS WILD-TYPE 105 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     13   24
  5Q LOSS WILD-TYPE  105  228
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              13               105
  MALE                24               228
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    31   1
  5Q LOSS WILD-TYPE 307   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     31    1
  5Q LOSS WILD-TYPE  307    8
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               31               307
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5Q LOSS MUTATED                         1                       33
  5Q LOSS WILD-TYPE                       2                      327
                   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                 2
  HEPATOCELLULAR CARCINOMA                      33               327
  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    34   1   0   2
  5Q LOSS WILD-TYPE 290  16   1  19
D51V10, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              34               290
  R1               1                16
  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    20
  5Q LOSS WILD-TYPE                                2   138
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           1    16
  5Q LOSS WILD-TYPE                        16   167
D51V11, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         20               138
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         16               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"
D51V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1  36
  5Q LOSS WILD-TYPE  15 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   36
  5Q LOSS WILD-TYPE   15  299
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              36               299
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    19  12
  6P LOSS WILD-TYPE 216 117
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               31               333 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12               117 
$`6P LOSS MUTATED`
TCGA-BC-A5W4 TCGA-DD-AADV TCGA-DD-AAEG TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       17.98        18.87        23.64        29.52         0.69        40.80 
TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H9 TCGA-BC-A69I TCGA-CC-A3M9 TCGA-CC-A5UD 
      120.82        56.91        22.92        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-A39X TCGA-DD-A39Z TCGA-DD-A4NH 
       12.95         6.02        33.04        55.69        19.76        30.15 
TCGA-DD-A4NK TCGA-DD-AAVU TCGA-ED-A66Y TCGA-G3-AAV6 TCGA-RC-A6M4 TCGA-UB-A7MB 
       39.78        72.39         9.73         2.14         0.72        19.76 
TCGA-UB-A7ME 
       15.98 

$`6P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        26.83        21.17        21.83 
TCGA-DD-AAEA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       18.90         9.96        22.62         8.12         6.38        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       30.74        22.13        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       31.27        12.72        24.56         0.76         7.04        10.32 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       27.88        40.41        49.84        47.74        18.25        20.81 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         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-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE 
        9.96        10.36        11.93        11.41         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-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B 
       79.73        37.78        83.57        53.33         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH 
       51.29        79.40        66.31        75.65        45.11        49.15 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A3A0 
       18.35        13.64        21.14        27.19         5.62        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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NJ 
       13.78        30.61        33.14        32.52        30.97        30.51 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-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        71.80        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-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-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       90.48        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        60.99 
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-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        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        11.64        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
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-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
       21.01         3.09         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
       19.04        15.39        15.52        36.10        27.88        16.44 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
        1.71        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        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 

  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=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P LOSS MUTATED        14        5         0          9          1          1
  6P LOSS WILD-TYPE     159       82         3         53          8          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P LOSS MUTATED          0         0         0
  6P LOSS WILD-TYPE        2         1         2
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 14               159
  STAGE II                 5                82
  STAGE III                0                 3
  STAGE IIIA               9                53
  STAGE IIIB               1                 8
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED    16   5  10   0
  6P LOSS WILD-TYPE 167  90  67  12
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              16               167
  T2               5                90
  T3              10                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"
D52V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    21   1
  6P LOSS WILD-TYPE 233   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     21    1
  6P LOSS WILD-TYPE  233    2
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              21               233
  1               1                 2
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    24   0
  6P LOSS WILD-TYPE 242   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     24    0
  6P LOSS WILD-TYPE  242    4
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              24               242
  1               0                 4
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    15  16
  6P LOSS WILD-TYPE 103 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     15   16
  6P LOSS WILD-TYPE  103  236
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              15               103
  MALE                16               236
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    25   1
  6P LOSS WILD-TYPE 313   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     25    1
  6P LOSS WILD-TYPE  313    8
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               25               313
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6P LOSS MUTATED                         0                       31
  6P LOSS WILD-TYPE                       3                      329
                   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                 3
  HEPATOCELLULAR CARCINOMA                      31               329
  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    28   2   0   1
  6P LOSS WILD-TYPE 296  15   1  20
D52V10, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              28               296
  R1               2                15
  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     8
  6P LOSS WILD-TYPE                                2   150
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           1    21
  6P LOSS WILD-TYPE                        16   162
D52V11, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          8               150
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                         21               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"
D52V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2  27
  6P LOSS WILD-TYPE  14 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   27
  6P LOSS WILD-TYPE   14  308
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              27               308
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    57  37
  6Q LOSS WILD-TYPE 178  92
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               94               270 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               37                92 
$`6Q LOSS MUTATED`
TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A5W4 TCGA-DD-A3A8 TCGA-DD-AADV TCGA-DD-AAEG 
       38.40         8.61        17.98         0.36        18.87        23.64 
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A6UC TCGA-T1-A6J8 TCGA-XR-A8TG 
       22.62         6.38        81.73        22.06         0.76        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
        0.69        40.80       120.82        56.91        20.81        22.92 
TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-A10Q TCGA-BC-A3KF TCGA-BC-A69I TCGA-CC-5260 
       17.10         1.51        37.32         0.26        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-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Z 
       45.11         6.02        33.04        18.35        55.69        19.76 
TCGA-DD-A3A1 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NS 
        7.66        33.14        30.15        30.51        39.78        80.75 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACH TCGA-DD-AACI 
       13.48         0.53        12.53        71.80         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-AADY TCGA-DD-AAE2 TCGA-DD-AAE9 TCGA-DD-AAVS TCGA-DD-AAVU 
       15.06        18.25        20.98        23.74        59.93        72.39 
TCGA-DD-AAVY TCGA-DD-AAW3 TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 
       64.77        53.69         9.73         0.20        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A2QR 
        1.84         0.20        18.74        11.93        60.89        19.10 
TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-AAV3 
       27.88        51.06        58.49        20.42        14.70        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5N0 TCGA-MI-A75E TCGA-MI-A75I TCGA-RC-A6M4 
        0.89         2.14        37.71        16.67        20.71         0.72 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-XR-A8TF 
       19.76        15.98        10.75        22.78 

$`6Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-BC-A110 TCGA-BC-A112 TCGA-BD-A3ER TCGA-DD-A4ND 
       83.24        11.74        69.57         5.03        36.66        90.28 
TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-EP-A3JL TCGA-FV-A3I1 
       26.83        21.17        21.83        18.90         9.96         8.12 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       30.74        22.13         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF TCGA-UB-AA0V TCGA-2Y-A9GS TCGA-2Y-A9GT 
       12.72        24.56         7.04        10.32        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H1 
       63.75        41.79        80.28        24.89        27.88        40.41 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       49.84        47.74        18.25         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-4073 
       10.78        10.59         0.66        14.76        48.99        27.91 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
       23.38         1.12        44.42        45.93        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 
       18.48        44.81        13.45         0.66         4.24         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.35         3.32        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-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-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        8.15        79.73        37.78        83.57        53.33         7.33 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH 
        0.46        51.29        79.40        66.31        75.65        49.15 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A2 
       13.64        21.14        27.19         5.62        25.81        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       32.52        30.97        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACA 
       22.78         1.45        35.67       114.35        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACJ TCGA-DD-AACK 
       76.41        55.40        12.00        15.42        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-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-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-AADO TCGA-DD-AADQ 
       35.67        35.05         0.39        29.52        14.89        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       66.67        15.58        18.21        19.30        18.25        18.15 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       18.61        19.99         4.64        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        90.48        89.69        82.62 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       80.71        76.18        56.48        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       60.99        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A26S TCGA-EP-A2KA 
        0.20        12.82        14.04        13.15        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3R3 TCGA-FV-A495 
       19.59         0.62        14.40        23.97        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.33         0.39        13.68        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       22.95        17.10        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       15.65        11.80        12.23        11.64        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.20         2.99        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G 
       27.25        29.79        13.97        12.03         9.57        22.95 
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-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        3.09         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        36.10        27.88        16.44         1.71 
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-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       33.86        30.41        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        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 
           19.430            20.055 
[1] "0.2 - 120.8 (19.4)" "0.0 - 114.3 (20.1)"
[1] "hr=" "1.2"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED        40       21         0         20          2          4
  6Q LOSS WILD-TYPE     133       66         3         42          7          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q LOSS MUTATED          0         0         1
  6Q LOSS WILD-TYPE        2         1         1
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 40               133
  STAGE II                21                66
  STAGE III                0                 3
  STAGE IIIA              20                42
  STAGE IIIB               2                 7
  STAGE IIIC               4                 3
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q LOSS MUTATED    44  24  22   3
  6Q LOSS WILD-TYPE 139  71  55   9
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              44               139
  T2              24                71
  T3              22                55
  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    65   2
  6Q LOSS WILD-TYPE 189   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     65    2
  6Q LOSS WILD-TYPE  189    1
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              65               189
  1               2                 1
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    73   1
  6Q LOSS WILD-TYPE 193   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     73    1
  6Q LOSS WILD-TYPE  193    3
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              73               193
  1               1                 3
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    38  56
  6Q LOSS WILD-TYPE  80 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     38   56
  6Q LOSS WILD-TYPE   80  196
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              38                80
  MALE                56               196
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    85   1
  6Q LOSS WILD-TYPE 253   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     85    1
  6Q LOSS WILD-TYPE  253    8
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               85               253
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6Q LOSS MUTATED                         0                       91
  6Q LOSS WILD-TYPE                       3                      269
                   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                 3
  HEPATOCELLULAR CARCINOMA                      91               269
  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    84   5   0   4
  6Q LOSS WILD-TYPE 240  12   1  17
D53V10, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              84               240
  R1               5                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
  6Q LOSS MUTATED                                  0    37
  6Q LOSS WILD-TYPE                                2   121
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           3    51
  6Q LOSS WILD-TYPE                        14   132
D53V11, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         37               121
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                         51               132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3  86
  6Q LOSS WILD-TYPE  13 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   86
  6Q LOSS WILD-TYPE   13  249
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              86               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 228 120
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               16               348 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                9               120 
$`7P LOSS MUTATED`
TCGA-FV-A3I1 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A5UD 
        8.12        45.93        22.36         3.19         9.86         9.99 
TCGA-CC-A7IG TCGA-DD-A1EF TCGA-DD-A39X TCGA-DD-AACB TCGA-DD-AADB TCGA-DD-AADN 
        9.83        12.95        55.69        76.41        40.83        29.52 
TCGA-EP-A2KB TCGA-K7-A5RG TCGA-RC-A7SK TCGA-WX-AA44 
       19.59        17.06        15.52        20.22 

$`7P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        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-A216 TCGA-BC-A3KF 
        2.99        25.32        23.38         1.12        44.42         0.26 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       14.60        12.72        18.48        44.81        13.45         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-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE 
        9.96        10.36        11.93        11.41         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
       21.34        12.00        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-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y 
       33.04        18.35        13.64        21.14        27.19         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
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-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        71.80        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-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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        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        60.99        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-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-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-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-A7M5 
       19.23        25.25        22.95        20.42        17.10        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        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 
       28.90         1.02         2.20         2.99        37.71        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
        0.30        21.04        19.33        19.04        15.39        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
       11.34         0.99        12.99        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        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            19.890 
[1] "3.2 - 76.4 (18.3)"  "0.0 - 120.8 (19.9)"
[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     164       82         3         60          9          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P LOSS MUTATED          0         0         0
  7P LOSS WILD-TYPE        2         1         2
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  9               164
  STAGE II                 5                82
  STAGE III                0                 3
  STAGE IIIA               2                60
  STAGE IIIB               0                 9
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P LOSS MUTATED     9   5   2   0
  7P LOSS WILD-TYPE 174  90  75  12
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               9               174
  T2               5                90
  T3               2                75
  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 244   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     10    0
  7P LOSS WILD-TYPE  244    3
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              10               244
  1               0                 3
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    11   0
  7P LOSS WILD-TYPE 255   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     11    0
  7P LOSS WILD-TYPE  255    4
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              11               255
  1               0                 4
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     8   8
  7P LOSS WILD-TYPE 110 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      8    8
  7P LOSS WILD-TYPE  110  244
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               8               110
  MALE                 8               244
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    14   1
  7P LOSS WILD-TYPE 324   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     14    1
  7P LOSS WILD-TYPE  324    8
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               14               324
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7P LOSS MUTATED                         0                       16
  7P LOSS WILD-TYPE                       3                      344
                   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                 3
  HEPATOCELLULAR CARCINOMA                      16               344
  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 310  17   1  19
D54V10, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              14               310
  R1               0                17
  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                                2   150
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           1     7
  7P LOSS WILD-TYPE                        16   176
D54V11, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          8               150
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                          7               176
[1] 4 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  15 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   14
  7P LOSS WILD-TYPE   15  321
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              14               321
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     8  13
  7Q LOSS WILD-TYPE 227 116
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               21               343 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               13               116 
$`7Q LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IG 
       45.93        22.36         3.19        11.41         9.99         9.83 
TCGA-DD-A1EF TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-AACB TCGA-DD-AACZ TCGA-DD-AADB 
       12.95        13.64        55.69        76.41         5.62        40.83 
TCGA-DD-AADF TCGA-DD-AADN TCGA-ED-A7PX TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-G3-A25S 
        3.78        29.52         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-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.76         7.04        10.32        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
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-A216 
       27.52         2.99        25.32        23.38         1.12        44.42 
TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        14.60        12.72        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        0.66         4.24         2.86         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UE 
        3.32         9.86         9.96        10.36        11.93         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-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-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y 
        6.02        33.04        18.35        21.14        27.19         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
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-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        71.80        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-AADC 
       42.58        44.22        22.09        40.08        40.54        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-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-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-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        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        90.48 
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        60.99 
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-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        9.73        12.82         0.20        14.04        13.15        13.41 
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-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
       12.03         0.03         0.33         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
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-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A6M5 
       58.88        26.27        17.69        21.01         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 
       10.75        11.34         0.99        12.99        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        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 

  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             20.12 
[1] "0.2 - 76.4 (13.6)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "2.5"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q LOSS MUTATED        11        7         0          3          0          0
  7Q LOSS WILD-TYPE     162       80         3         59          9          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q LOSS MUTATED          0         0         0
  7Q LOSS WILD-TYPE        2         1         2
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 11               162
  STAGE II                 7                80
  STAGE III                0                 3
  STAGE IIIA               3                59
  STAGE IIIB               0                 9
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED    11   7   3   0
  7Q LOSS WILD-TYPE 172  88  74  12
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              11               172
  T2               7                88
  T3               3                74
  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    13   0
  7Q LOSS WILD-TYPE 241   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     13    0
  7Q LOSS WILD-TYPE  241    3
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              13               241
  1               0                 3
[1] 2 2
[1] FALSE
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    16   0
  7Q LOSS WILD-TYPE 250   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     16    0
  7Q LOSS WILD-TYPE  250    4
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              16               250
  1               0                 4
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    11  10
  7Q LOSS WILD-TYPE 107 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11   10
  7Q LOSS WILD-TYPE  107  242
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              11               107
  MALE                10               242
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    19   1
  7Q LOSS WILD-TYPE 319   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     19    1
  7Q LOSS WILD-TYPE  319    8
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               19               319
  YES               1                 8
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7Q LOSS MUTATED                         0                       21
  7Q LOSS WILD-TYPE                       3                      339
                   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                 3
  HEPATOCELLULAR CARCINOMA                      21               339
  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    17   1   0   3
  7Q LOSS WILD-TYPE 307  16   1  18
D55V10, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              17               307
  R1               1                16
  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    11
  7Q LOSS WILD-TYPE                                2   147
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           3     7
  7Q LOSS WILD-TYPE                        14   176
D55V11, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         11               147
  BLACK OR AFRICAN AMERICAN                      3                14
  WHITE                                          7               176
[1] 4 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  15 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   19
  7Q LOSS WILD-TYPE   15  316
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              19               316
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   131  62
  8P LOSS WILD-TYPE 104  67
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              193               171 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               62                67 
$`8P LOSS MUTATED`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A112 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI 
       11.74        38.40         5.03         0.36        90.28        26.83 
TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       18.87        21.17        21.83        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-KR-A7K7 
       81.73        30.74        22.13        22.06         1.84        31.27 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GU 
        0.76         7.04        29.52        40.80        23.80        63.75 
TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9HA 
       80.28        56.91        49.84        47.74        18.25         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q 
        8.55        13.02        17.10         1.51        48.99        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       10.13        27.52        27.52        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 
       22.36        14.60        12.72        13.45         0.66         3.19 
TCGA-CC-5262 TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL 
        3.39         7.13         9.83        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-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A1EE TCGA-DD-A1EG 
       83.57        53.33       113.00        21.76        11.47        45.11 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       33.04        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH 
       25.81        17.59        13.78        30.61        33.14        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       30.51        39.78        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACC 
       22.78         1.45        35.67       114.35        76.41        55.40 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       71.80        15.42         6.41        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACY TCGA-DD-AAD0 
       13.64        14.20        59.31        51.52        47.67         4.50 
TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADG 
       42.58        40.08        40.54        40.83        13.97        37.64 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.67        34.49         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AAE0 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       14.33        66.67        18.25        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       15.72        25.08        26.63        25.78        50.33        90.48 
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-AAW3 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       62.47        66.25        53.69        13.35        12.82         0.20 
TCGA-ED-A7XO TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HT 
       14.04        18.74        19.99        20.61        11.93        14.40 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25V 
       23.97        19.10        27.88         0.03        13.68        28.27 
TCGA-G3-A3CJ TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 
       19.53        14.70        20.78        15.65        12.23         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-LG-A9QC 
       11.64         2.14        11.87         2.99        16.83        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF 
       12.03         9.57        16.67        20.71        10.85        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SF 
       17.69        21.01         3.09         0.30        21.04        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       15.39        15.52        36.10        19.76         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WX-AA47 TCGA-XR-A8TD TCGA-YA-A8S7 TCGA-ZP-A9CV 
       10.75        11.34        18.28        33.86        13.55        35.77 
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 

$`8P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-AAEA 
       83.24         8.61        69.57        17.98        36.66        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H 
       23.64         9.96        20.75         2.14        12.72        24.56 
TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       10.32         0.69        53.39        41.79        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-5C-A9VG TCGA-5C-A9VH 
      120.82        40.41        20.81        22.92        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X 
        0.66        14.76        27.91        46.78         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5258 TCGA-CC-5260 
       23.38         1.12        18.48        44.81         4.24         2.86 
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-A7IH 
       11.93        11.41         9.99         8.94        21.34        12.00 
TCGA-CC-A7IK TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
        8.61        37.78         7.33         2.60         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       90.71        79.40        66.31        19.79        75.65        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A3A1 TCGA-DD-A3A2 
       49.15         6.02        18.35        27.19         7.66        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NL 
       20.12       102.74       107.11        32.52        30.97        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-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACF 
       13.48         0.53        11.41        75.65        12.53        12.00 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACV 
       53.19        69.11         0.30         3.52        51.35        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 
       46.82         5.59         5.62        18.54        21.63        44.22 
TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADL 
       22.09        40.47        39.52         3.78        35.05        20.91 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
       15.58        18.21        19.30        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-DD-AAW2 
       18.61        35.08        80.71        56.48        65.39        60.99 
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-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KB 
       13.15        13.41        13.35         1.84         0.20        19.59 
TCGA-EP-A2KC TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T 
        0.62        60.89        12.03         0.33         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M7 
       19.23        25.25        22.95        20.42        17.10        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       14.14        15.78        11.80        13.55        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
        2.20        37.71        17.06        11.80        27.25        29.79 
TCGA-MI-A75G TCGA-MR-A520 TCGA-NI-A4U2 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7SB 
       22.95         7.53        58.88         0.72         0.49        19.33 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       27.88        16.44         0.99        12.99        20.22        24.85 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CY 
       30.41        22.78        25.71 

  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 
            20.61             19.30 
[1] "0.0 - 114.3 (20.6)" "0.2 - 120.8 (19.3)"
[1] "hr=" "1.3"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P LOSS MUTATED        91       49         0         29          8          4
  8P LOSS WILD-TYPE      82       38         3         33          1          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P LOSS MUTATED          1         0         1
  8P LOSS WILD-TYPE        1         1         1
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 91                82
  STAGE II                49                38
  STAGE III                0                 3
  STAGE IIIA              29                33
  STAGE IIIB               8                 1
  STAGE IIIC               4                 3
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED   97 56 38  5
  8P LOSS WILD-TYPE 86 39 39  7
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              97                86
  T2              56                39
  T3              38                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   129   2
  8P LOSS WILD-TYPE 125   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    129    2
  8P LOSS WILD-TYPE  125    1
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             129               125
  1               2                 1
[1] 2 2
[1] FALSE
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   138   2
  8P LOSS WILD-TYPE 128   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    138    2
  8P LOSS WILD-TYPE  128    2
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             138               128
  1               2                 2
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    61 135
  8P LOSS WILD-TYPE  57 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     61  135
  8P LOSS WILD-TYPE   57  117
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              61                57
  MALE               135               117
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   181   5
  8P LOSS WILD-TYPE 157   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    181    5
  8P LOSS WILD-TYPE  157    4
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              181               157
  YES               5                 4
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8P LOSS MUTATED                         1                      194
  8P LOSS WILD-TYPE                       2                      166
                   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                        1                 2
  HEPATOCELLULAR CARCINOMA                     194               166
  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   171  11   0  10
  8P LOSS WILD-TYPE 153   6   1  11
D56V10, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             171               153
  R1              11                 6
  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
  8P LOSS MUTATED                                  1    80
  8P LOSS WILD-TYPE                                1    78
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          12    98
  8P LOSS WILD-TYPE                         5    85
D56V11, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                         80                78
  BLACK OR AFRICAN AMERICAN                     12                 5
  WHITE                                         98                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    10 176
  8P LOSS WILD-TYPE   6 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     10  176
  8P LOSS WILD-TYPE    6  159
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                 6
  NOT HISPANIC OR LATINO             176               159
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    29  15
  8Q LOSS WILD-TYPE 206 114
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               44               320 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               114 
$`8Q LOSS MUTATED`
TCGA-DD-AADV TCGA-G3-A7M9 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-2Y-A9GS TCGA-2Y-A9GU 
       18.87         1.84         0.76         7.04        23.80        63.75 
TCGA-2Y-A9GX TCGA-5R-AAAM TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KG TCGA-BW-A5NO 
       80.28         1.51        27.52        45.93        22.36         0.66 
TCGA-CC-5261 TCGA-CC-A7IE TCGA-CC-A8HU TCGA-DD-A115 TCGA-DD-A3A0 TCGA-DD-A3A9 
        3.19         7.13        11.31        83.57        25.81        30.61 
TCGA-DD-A4NA TCGA-DD-A4NK TCGA-DD-A73C TCGA-DD-AACE TCGA-DD-AACY TCGA-DD-AAD0 
       33.14        39.78        23.05        71.80        47.67         4.50 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADP TCGA-DD-AADW TCGA-DD-AAE6 TCGA-DD-AAEB 
       40.08        40.54        15.06        19.30         4.64        15.72 
TCGA-DD-AAED TCGA-DD-AAVU TCGA-ED-A7PY TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25V 
       25.08        72.39        12.82        27.88         0.03        28.27 
TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A6M6 
       12.23         0.89         2.14        26.27         3.09         0.30 
TCGA-RC-A7S9 TCGA-ZS-A9CF 
       21.04        79.30 

$`8Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 
       17.98        36.66         0.36        90.28        26.83        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
        6.38        81.73        30.74        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG 
        2.14        31.27        12.72        24.56        10.32        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ 
        0.69        40.80        53.39        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-4073 
       10.59         0.66        17.10        14.76        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A69I 
       23.38         1.12        44.42         0.26        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 
       18.48        44.81        13.45         4.24         2.86         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-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
       12.00        13.12        12.56         8.61         9.14         4.60 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 
        9.17         6.94         8.15        79.73        37.78        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        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-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-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL 
       13.78        32.52        30.97        30.15        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-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93         9.30        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-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       46.82         5.59         5.62        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       44.22        22.09        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-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        14.89        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       18.21        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       19.99        23.74        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       90.48        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        60.99 
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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        9.73         0.20         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       19.10        12.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-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-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        11.64        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       22.95        20.71         7.53        10.85        58.88        17.69 
TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       21.01         0.72         0.49        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        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-A9CG 
       45.57        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 
            21.70             19.76 
[1] "0.0 - 83.6 (21.7)"  "0.2 - 120.8 (19.8)"
[1] "hr=" "1"  
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q LOSS MUTATED        19       11         0          9          1          1
  8Q LOSS WILD-TYPE     154       76         3         53          8          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q LOSS MUTATED          0         0         1
  8Q LOSS WILD-TYPE        2         1         1
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 19               154
  STAGE II                11                76
  STAGE III                0                 3
  STAGE IIIA               9                53
  STAGE IIIB               1                 8
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                1                 1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED    20  13  10   2
  8Q LOSS WILD-TYPE 163  82  67  10
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              20               163
  T2              13                82
  T3              10                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"
D57V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    27   1
  8Q LOSS WILD-TYPE 227   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     27    1
  8Q LOSS WILD-TYPE  227    2
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              27               227
  1               1                 2
[1] 2 2
[1] FALSE
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    34   1
  8Q LOSS WILD-TYPE 232   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     34    1
  8Q LOSS WILD-TYPE  232    3
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              34               232
  1               1                 3
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    20  25
  8Q LOSS WILD-TYPE  98 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     20   25
  8Q LOSS WILD-TYPE   98  227
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              20                98
  MALE                25               227
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    40   0
  8Q LOSS WILD-TYPE 298   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     40    0
  8Q LOSS WILD-TYPE  298    9
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               40               298
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8Q LOSS MUTATED                         0                       44
  8Q LOSS WILD-TYPE                       3                      316
                   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                 3
  HEPATOCELLULAR CARCINOMA                      44               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
  8Q LOSS MUTATED    38   3   0   4
  8Q LOSS WILD-TYPE 286  14   1  17
D57V10, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              38               286
  R1               3                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
  8Q LOSS MUTATED                                  0    18
  8Q LOSS WILD-TYPE                                2   140
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           2    25
  8Q LOSS WILD-TYPE                        15   158
D57V11, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         18               140
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         25               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"
D57V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  42
  8Q LOSS WILD-TYPE  15 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   42
  8Q LOSS WILD-TYPE   15  293
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              42               293
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    71  46
  9P LOSS WILD-TYPE 164  83
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              117               247 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               46                83 
$`9P LOSS MUTATED`
TCGA-2Y-A9H6 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       11.74         5.03        17.98        90.28        26.83        18.87 
TCGA-DD-AAE8 TCGA-FV-A3I1 TCGA-T1-A6J8 TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GY 
       21.83         8.12         0.76        23.80        63.75        24.89 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-3K-AAZ8 
       56.91        49.84        18.25        20.81        22.92        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       10.78        10.59        48.99        37.32        10.13        46.78 
TCGA-BC-A10U TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT 
       27.52        45.93        14.60         4.24         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF 
        9.86        10.36        11.93         9.99         8.94        21.34 
TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW 
        9.83        12.56         9.14        11.31         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       79.73        83.57        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-A3A0 TCGA-DD-A3A9 TCGA-DD-A4NO TCGA-DD-AA3A 
       55.69         5.62        25.81        30.61        73.81        13.48 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACW 
       71.80        15.42        61.68        13.64        51.52        46.82 
TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AADC TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADO 
        5.62        42.58        13.97        34.49        20.91        14.89 
TCGA-DD-AADP TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEE 
       15.06        18.15        18.61         4.64        25.08        26.63 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 
       35.08        89.69        72.39        76.18        62.47        66.25 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A2KC 
       29.92        13.35         0.20        13.15         0.20         0.62 
TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A7M5 TCGA-G3-AAV1 
       11.93        23.97        13.68        51.06        14.70        11.80 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K8 TCGA-MI-A75G TCGA-MI-A75I 
        2.14        11.87         2.20        29.79        22.95        20.71 
TCGA-NI-A8LF TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF 
       26.27         0.72         0.49         0.30        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 
       15.39        15.52        36.10        15.98        10.75         0.99 
TCGA-WQ-AB4B TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       12.99        35.87        25.15 

$`9P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A3A8 
       83.24        38.40         8.61        69.57        36.66         0.36 
TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 
       21.17        18.90        23.64         9.96        22.62         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF TCGA-UB-AA0V 
        2.14        31.27        12.72        24.56         7.04        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX 
       29.52         0.69        40.80        53.39        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       27.88       120.82        40.41        47.74         1.18         8.55 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10T 
        0.66        17.10        14.76         1.51        27.91        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF 
        2.99        25.32        23.38         1.12        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        12.72        18.48        44.81        13.45         0.66 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A3MA TCGA-CC-A5UC 
        2.86         3.19         3.39         3.35         9.96        11.41 
TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV 
        7.13        12.00        13.12         8.61         4.60         9.17 
TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
       37.78       113.00        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V 
       19.79        75.65        11.47        49.15        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       27.19        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        13.78        33.14        32.52        30.97 
TCGA-DD-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-AAC8 
       23.05        22.78         1.45        35.67       114.35         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       11.41        75.65        76.41        55.40        12.53        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACX 
       42.81        14.20        59.31        51.35        50.33         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 
       47.67         4.50        18.54        21.63        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.08        40.54        40.83        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ 
       37.64        35.67        35.05         0.39        29.52        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-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEH TCGA-DD-AAEI 
       20.98        19.99        23.74        15.72        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY 
       90.48        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        60.99        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-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HT 
        1.84        18.74        19.99        20.61        19.59        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       60.89        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39        53.79        28.27        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-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       20.42        17.10        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        11.64        28.90 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 
       27.25        13.97        12.03         9.57        16.67         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       10.85        58.88        17.69        21.01         3.09        21.04 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-WJ-A86L TCGA-WX-AA44 
       27.88        19.76        16.44         1.71        11.34        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       35.77        25.71        23.21        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       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 
            17.98             20.75 
[1] "0.2 - 90.3 (18.0)"  "0.0 - 120.8 (20.8)"
[1] "hr=" "1.4"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P LOSS MUTATED        51       27         0         21          2          2
  9P LOSS WILD-TYPE     122       60         3         41          7          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P LOSS MUTATED          1         1         2
  9P LOSS WILD-TYPE        1         0         0
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 51               122
  STAGE II                27                60
  STAGE III                0                 3
  STAGE IIIA              21                41
  STAGE IIIB               2                 7
  STAGE IIIC               2                 5
  STAGE IV                 1                 1
  STAGE IVA                1                 0
  STAGE IVB                2                 0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P LOSS MUTATED    56  32  27   4
  9P LOSS WILD-TYPE 127  63  50   8
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              56               127
  T2              32                63
  T3              27                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"
D58V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    82   2
  9P LOSS WILD-TYPE 172   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     82    2
  9P LOSS WILD-TYPE  172    1
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              82               172
  1               2                 1
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    86   3
  9P LOSS WILD-TYPE 180   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     86    3
  9P LOSS WILD-TYPE  180    1
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              86               180
  1               3                 1
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    31  88
  9P LOSS WILD-TYPE  87 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     31   88
  9P LOSS WILD-TYPE   87  164
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              31                87
  MALE                88               164
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   106   2
  9P LOSS WILD-TYPE 232   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    106    2
  9P LOSS WILD-TYPE  232    7
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              106               232
  YES               2                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9P LOSS MUTATED                         1                      116
  9P LOSS WILD-TYPE                       2                      244
                   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                        1                 2
  HEPATOCELLULAR CARCINOMA                     116               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
  9P LOSS MUTATED   101   8   1   7
  9P LOSS WILD-TYPE 223   9   0  14
D58V10, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             101               223
  R1               8                 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                                2    99
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           6    53
  9P LOSS WILD-TYPE                        11   130
D58V11, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         59                99
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         53               130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2 113
  9P LOSS WILD-TYPE  14 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2  113
  9P LOSS WILD-TYPE   14  222
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO             113               222
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    65  43
  9Q LOSS WILD-TYPE 170  86
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              108               256 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               43                86 
$`9Q LOSS MUTATED`
TCGA-2Y-A9H6 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 
       11.74         5.03        17.98        26.83        18.87        21.83 
TCGA-DD-AAEA TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-2Y-A9GS 
       18.90         8.12         6.38         0.76         7.04        23.80 
TCGA-2Y-A9GU TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       63.75        56.91        49.84        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R 
        1.18        13.02        10.78        10.59        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 
       46.78        27.52        45.93        14.60         4.24         2.86 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UE 
        4.24         3.32         9.86        10.36        11.93         8.94 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A9FW TCGA-DD-A113 
       21.34         9.83        12.56         9.14         8.15        79.73 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF 
       53.33         7.33         2.60         0.46        21.76        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y 
       45.11         6.02        33.04        18.35        55.69         5.62 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACE 
       30.61        33.14        73.81        13.48        76.41        71.80 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD8 
       61.68        13.64        51.52         5.62        42.58        40.08 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ 
       34.49        20.91        14.89        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-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CH TCGA-G3-A7M5 TCGA-G3-AAV1 
       12.03        13.68        51.06        25.64        14.70        11.80 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF 
        2.14        11.87         2.20        22.95        20.71        26.27 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.49         0.30        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-AB4B TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       36.10        15.98        10.75        12.99        35.87        25.15 

$`9Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A3A8 
       83.24        38.40         8.61        69.57        36.66         0.36 
TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A4ZP 
       90.28        21.17        23.64         9.96        22.62        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       30.74        22.13        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 
       31.27        12.72        24.56        10.32        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       40.80        53.39        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9HB TCGA-5C-AAPD TCGA-5R-AA1C 
      120.82        40.41        47.74         8.55         0.66        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10T TCGA-BC-A10W 
       14.76         1.51        48.99        27.91        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
       25.32        23.38         1.12        44.42         0.26        22.36 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 
       12.72        18.48        44.81        13.45         0.66         3.19 
TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE 
        3.39         3.35         9.96        11.41         9.99         7.13 
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-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
      114.35         0.53        11.41        75.65        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-AACQ TCGA-DD-AACS TCGA-DD-AACT 
        3.52        58.16        42.81        14.20        59.31        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-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       21.63        44.22        22.09        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE 
       18.61        19.99         4.64        23.74        15.72        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV 
       25.78        50.33        90.48        82.62        59.93        80.71 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       56.48        64.77        65.39        60.99        53.69        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       28.08        13.91         9.73         0.20        12.82        14.04 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A495 
       20.61        19.59        14.40        60.89        19.10         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.33         0.39        53.79        28.27        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       21.53         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       20.42        17.10        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        11.64        28.90 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
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-A6M4 TCGA-RC-A7S9 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
        0.72        21.04        27.88        19.76        16.44         1.71 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
       11.34         0.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        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 
           18.115            20.515 
[1] "0.2 - 89.7 (18.1)"  "0.0 - 120.8 (20.5)"
[1] "hr=" "1.4"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED        46       26         0         17          2          4
  9Q LOSS WILD-TYPE     127       61         3         45          7          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q LOSS MUTATED          1         1         2
  9Q LOSS WILD-TYPE        1         0         0
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 46               127
  STAGE II                26                61
  STAGE III                0                 3
  STAGE IIIA              17                45
  STAGE IIIB               2                 7
  STAGE IIIC               4                 3
  STAGE IV                 1                 1
  STAGE IVA                1                 0
  STAGE IVB                2                 0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED    51  32  22   5
  9Q LOSS WILD-TYPE 132  63  55   7
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              51               132
  T2              32                63
  T3              22                55
  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    71   3
  9Q LOSS WILD-TYPE 183   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     71    3
  9Q LOSS WILD-TYPE  183    0
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              71               183
  1               3                 0
[1] 2 2
[1] FALSE
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    75   3
  9Q LOSS WILD-TYPE 191   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     75    3
  9Q LOSS WILD-TYPE  191    1
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              75               191
  1               3                 1
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    30  80
  9Q LOSS WILD-TYPE  88 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     30   80
  9Q LOSS WILD-TYPE   88  172
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              30                88
  MALE                80               172
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    98   2
  9Q LOSS WILD-TYPE 240   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     98    2
  9Q LOSS WILD-TYPE  240    7
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               98               240
  YES               2                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9Q LOSS MUTATED                         1                      107
  9Q LOSS WILD-TYPE                       2                      253
                   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                        1                 2
  HEPATOCELLULAR CARCINOMA                     107               253
  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    93   6   1   8
  9Q LOSS WILD-TYPE 231  11   0  13
D59V10, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              93               231
  R1               6                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
  9Q LOSS MUTATED                                  0    52
  9Q LOSS WILD-TYPE                                2   106
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           6    52
  9Q LOSS WILD-TYPE                        11   131
D59V11, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         52               106
  BLACK OR AFRICAN AMERICAN                      6                11
  WHITE                                         52               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2 106
  9Q LOSS WILD-TYPE  14 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2  106
  9Q LOSS WILD-TYPE   14  229
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO             106               229
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    34  12
  10P LOSS WILD-TYPE 201 117
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                46                318 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                117 
$`10P LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-KR-A7K7 TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        5.03        17.98        26.83        31.27         0.69        40.80 
TCGA-2Y-A9H2 TCGA-BC-A217 TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       56.91        45.93        18.48        44.81        13.45         0.66 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A7II TCGA-DD-A11C TCGA-DD-A39Y 
        9.86         9.96        11.93        13.12        21.76         5.62 
TCGA-DD-A4NQ TCGA-DD-AACG TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACU TCGA-DD-AACV 
       12.26        15.42        58.16        61.68        51.52        50.33 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADR TCGA-DD-AAVU TCGA-ED-A66Y TCGA-ED-A7PX 
       40.08        40.54        66.67        72.39         9.73         0.20 
TCGA-ED-A7XO TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A25X TCGA-G3-A7M5 
       14.04         0.20        23.97        27.88        58.49        14.70 
TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-NI-A4U2 TCGA-QA-A7B7 
       11.80         0.89        17.06        27.25        58.88         3.09 
TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-XR-A8TD TCGA-ZS-A9CF 
       36.10         0.99        33.86        79.30 

$`10P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
        0.36        90.28        18.87        21.17        21.83        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       23.64         9.96        22.62         8.12         6.38        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       30.74        22.13        22.06         1.84        20.75         2.14 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       12.72        24.56         0.76         7.04        10.32        29.52 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        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-A216 TCGA-BC-A3KF 
        2.99        25.32        23.38         1.12        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       22.36        14.60        12.72         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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       30.61        33.14        32.52        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR 
       39.78        56.25        29.56        73.81       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        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        71.80        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN 
        6.41        53.19        69.11         0.30         3.52        42.81 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX 
       13.64        14.20        59.31        51.35        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       44.22        22.09        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-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        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        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       26.93        28.08        13.91        13.35        12.82         0.20 
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-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       19.10        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        28.27        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-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       17.10        20.78        11.87        14.14        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        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.20         2.99        37.71        16.83        11.80 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71         7.53        10.85        26.27        17.69        21.01 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        10.75        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       18.28        30.41        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-A9CG 
       23.21        35.87        25.15        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 
            20.120             19.775 
[1] "0.2 - 79.3 (20.1)"  "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        16       14         0         10          1
  10P LOSS WILD-TYPE     157       73         3         52          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P LOSS MUTATED            2        0         0         0
  10P LOSS WILD-TYPE          5        2         1         2
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  16                157
  STAGE II                 14                 73
  STAGE III                 0                  3
  STAGE IIIA               10                 52
  STAGE IIIB                1                  8
  STAGE IIIC                2                  5
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P LOSS MUTATED    17  15  13   2
  10P LOSS WILD-TYPE 166  80  64  10
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               17                166
  T2               15                 80
  T3               13                 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"
D60V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    29   0
  10P LOSS WILD-TYPE 225   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     29    0
  10P LOSS WILD-TYPE  225    3
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               29                225
  1                0                  3
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    34   0
  10P LOSS WILD-TYPE 232   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     34    0
  10P LOSS WILD-TYPE  232    4
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               34                232
  1                0                  4
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    15  32
  10P LOSS WILD-TYPE 103 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     15   32
  10P LOSS WILD-TYPE  103  220
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               15                103
  MALE                 32                220
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    46   0
  10P LOSS WILD-TYPE 292   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     46    0
  10P LOSS WILD-TYPE  292    9
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                46                292
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10P LOSS MUTATED                         0                       44
  10P LOSS WILD-TYPE                       3                      316
                    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                  3
  HEPATOCELLULAR CARCINOMA                       44                316
  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    42   1   0   4
  10P LOSS WILD-TYPE 282  16   1  17
D60V10, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               42                282
  R1                1                 16
  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    21
  10P LOSS WILD-TYPE                                2   137
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           5    21
  10P LOSS WILD-TYPE                        12   162
D60V11, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          21                137
  BLACK OR AFRICAN AMERICAN                       5                 12
  WHITE                                          21                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"
D60V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2  41
  10P LOSS WILD-TYPE  14 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   41
  10P LOSS WILD-TYPE   14  294
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               41                294
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    48  29
  10Q LOSS WILD-TYPE 187 100
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                77                287 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                29                100 
$`10Q LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AAE8 TCGA-KR-A7K7 TCGA-ZP-A9D1 
        5.03        17.98        26.83        21.83        31.27         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-5C-AAPD TCGA-BC-A10Q 
       40.80        23.80        56.91        47.74         0.66        37.32 
TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A217 TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       10.13         2.99        45.93        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.66         2.86         3.35         3.32         9.86         9.96 
TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A8HT TCGA-DD-A114 
       11.93         9.99         8.94        13.12         4.60        37.78 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A4NQ 
        2.60        21.76        45.11        13.64         5.62        12.26 
TCGA-DD-AACG TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACV 
       15.42        58.16        61.68        14.20        51.52        50.33 
TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADL 
        5.62        42.58        44.22        40.08        40.54        20.91 
TCGA-DD-AADR TCGA-DD-AADY TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO 
       66.67        18.25        29.92         9.73         0.20        14.04 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25U 
        1.84         0.20        23.97        27.88         0.33        53.79 
TCGA-G3-A25X TCGA-G3-A5SJ TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-K7-A5RG 
       58.49        22.95        14.70        11.80         0.89        17.06 
TCGA-KR-A7K2 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-QA-A7B7 TCGA-RC-A6M6 TCGA-RC-A7SB 
       27.25        10.85        58.88         3.09         0.30        19.33 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MD TCGA-WQ-A9G7 TCGA-XR-A8TD 
       15.52        36.10         1.71         0.99        33.86 

$`10Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG 
        0.36        90.28        18.87        21.17        18.90        23.64 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
        9.96        22.62         8.12         6.38        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG 
       22.13        22.06         1.84        20.75         2.14        12.72 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-2Y-A9GT 
       24.56         0.76         7.04        10.32        29.52        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       63.75        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       40.41        49.84        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55        13.02        10.78        10.59        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
        1.51        48.99        27.91        46.78        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
       25.32        23.38         1.12        44.42         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       14.60        12.72         4.24         3.19         3.39         4.24 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       10.36        11.41         7.13        21.34         9.83        12.00 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       12.56         8.61         9.14        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        8.15        79.73        83.57        53.33       113.00         7.33 
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-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        11.47        12.95        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78        30.61        33.14        32.52        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-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        71.80 
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-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX 
       42.81        13.64        59.31        51.35        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADB 
       47.67         4.50        18.54        21.63        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-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       14.33        15.58        18.21        19.30        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        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        90.48 
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        60.99 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       53.69        26.93        28.08        13.91        13.35        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20        13.15        13.41        13.35        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       19.10        12.03         0.03         0.39        13.68        51.06 
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-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.23        25.25        20.42        17.10        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 
       14.14        15.78        15.65        12.23        13.55        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       37.71        16.83        11.80        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A8LF 
        9.57        16.67        22.95        20.71         7.53        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SF 
       17.69        21.01         0.72         0.49        21.04        19.04 
TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-AA0U 
       15.39        27.88        19.76        16.44        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE 
       11.34        12.99        20.22        24.85        18.28        30.41 
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-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        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              20.42 
[1] "0.2 - 66.7 (15.5)"  "0.0 - 120.8 (20.4)"
[1] "hr=" "1.4"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED        31       19         0         15          2
  10Q LOSS WILD-TYPE     142       68         3         47          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q LOSS MUTATED            3        0         0         0
  10Q LOSS WILD-TYPE          4        2         1         2
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  31                142
  STAGE II                 19                 68
  STAGE III                 0                  3
  STAGE IIIA               15                 47
  STAGE IIIB                2                  7
  STAGE IIIC                3                  4
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED    32  22  19   5
  10Q LOSS WILD-TYPE 151  73  58   7
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               32                151
  T2               22                 73
  T3               19                 58
  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    53   0
  10Q LOSS WILD-TYPE 201   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     53    0
  10Q LOSS WILD-TYPE  201    3
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               53                201
  1                0                  3
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    59   0
  10Q LOSS WILD-TYPE 207   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     59    0
  10Q LOSS WILD-TYPE  207    4
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               59                207
  1                0                  4
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    23  55
  10Q LOSS WILD-TYPE  95 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     23   55
  10Q LOSS WILD-TYPE   95  197
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               23                 95
  MALE                 55                197
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    73   1
  10Q LOSS WILD-TYPE 265   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     73    1
  10Q LOSS WILD-TYPE  265    8
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                73                265
  YES                1                  8
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10Q LOSS MUTATED                         1                       73
  10Q LOSS WILD-TYPE                       2                      287
                    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                  2
  HEPATOCELLULAR CARCINOMA                       73                287
  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    66   4   0   7
  10Q LOSS WILD-TYPE 258  13   1  14
D61V10, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               66                258
  R1                4                 13
  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    40
  10Q LOSS WILD-TYPE                                2   118
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          10    28
  10Q LOSS WILD-TYPE                         7   155
D61V11, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          40                118
  BLACK OR AFRICAN AMERICAN                      10                  7
  WHITE                                          28                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3  70
  10Q LOSS WILD-TYPE  13 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3   70
  10Q LOSS WILD-TYPE   13  265
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               70                265
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    36  24
  11P LOSS WILD-TYPE 199 105
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                60                304 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                105 
$`11P LOSS MUTATED`
TCGA-2Y-A9H6 TCGA-BC-A112 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-FV-A4ZP TCGA-G3-A7M9 
       11.74         5.03        90.28        26.83        81.73         1.84 
TCGA-KR-A7K7 TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       31.27        23.80        24.89        49.84        13.02        10.78 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A217 TCGA-CC-5264 
        0.66        14.76        37.32        46.78        45.93         3.35 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A7IK TCGA-CC-A7IL TCGA-DD-A113 
        9.86         9.96        11.93         8.61         9.14        79.73 
TCGA-DD-A115 TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB 
       83.57        90.71        12.95        33.04        55.69        32.52 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADN 
       61.68        13.64        44.22        22.09        40.47        29.52 
TCGA-DD-AADO TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 
       14.89        18.61        35.08         0.20        14.04         1.84 
TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A5SJ TCGA-G3-AAV1 
        0.62        23.97         0.33        13.68        22.95        11.80 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-KR-A7K2 TCGA-MI-A75G TCGA-RC-A6M4 TCGA-RC-A6M5 
        2.14        11.87        27.25        22.95         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-YA-A8S7 
        0.30        19.33        36.10        27.88        16.44        13.55 

$`11P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BD-A3ER 
       83.24        38.40         8.61        69.57        17.98        36.66 
TCGA-DD-A3A8 TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG 
        0.36        18.87        21.17        21.83        18.90        23.64 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG 
        9.96        22.62         8.12         6.38        30.74        22.13 
TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       22.06        20.75         2.14        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT 
        7.04        10.32        29.52         0.69        40.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        41.79        80.28        27.88       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       56.91        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
        8.55        10.59        17.10         1.51        48.99        27.91 
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-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
        1.12        44.42         0.26        22.36        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       18.48        44.81        13.45         0.66         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A5UC 
        3.19         3.39         4.24         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-A7II TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       13.12        12.56         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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       13.78        30.61        33.14        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
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-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-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15        20.98        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        26.63        25.78        50.33        90.48        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        60.99        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-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20        12.82        13.15        13.41        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61        19.59        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       60.89        19.10        27.88        12.03         0.03         0.39 
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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL 
       25.64         5.92        19.53        19.23        25.25        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        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        11.64        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       11.80        29.79        13.97        12.03         9.57        16.67 
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-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       21.01         3.09        21.04        19.04        15.39        15.52 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       19.76         1.71        15.98        10.75        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
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-A9CF TCGA-ZS-A9CG 
       12.99        45.57        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 
            17.525             19.990 
[1] "0.2 - 90.7 (17.5)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.3"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P LOSS MUTATED        19       17         0         17          2
  11P LOSS WILD-TYPE     154       70         3         45          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P LOSS MUTATED            2        1         1         0
  11P LOSS WILD-TYPE          5        1         0         2
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  19                154
  STAGE II                 17                 70
  STAGE III                 0                  3
  STAGE IIIA               17                 45
  STAGE IIIB                2                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P LOSS MUTATED    21  20  21   1
  11P LOSS WILD-TYPE 162  75  56  11
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               21                162
  T2               20                 75
  T3               21                 56
  T4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    41   2
  11P LOSS WILD-TYPE 213   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     41    2
  11P LOSS WILD-TYPE  213    1
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               41                213
  1                2                  1
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    47   1
  11P LOSS WILD-TYPE 219   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     47    1
  11P LOSS WILD-TYPE  219    3
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               47                219
  1                1                  3
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    19  44
  11P LOSS WILD-TYPE  99 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     19   44
  11P LOSS WILD-TYPE   99  208
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               19                 99
  MALE                 44                208
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    55   1
  11P LOSS WILD-TYPE 283   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     55    1
  11P LOSS WILD-TYPE  283    8
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                55                283
  YES                1                  8
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11P LOSS MUTATED                         2                       58
  11P LOSS WILD-TYPE                       1                      302
                    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                         2                  1
  HEPATOCELLULAR CARCINOMA                       58                302
  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   6   0   3
  11P LOSS WILD-TYPE 270  11   1  18
D62V10, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               54                270
  R1                6                 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                                  1    23
  11P LOSS WILD-TYPE                                1   135
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           3    36
  11P LOSS WILD-TYPE                        14   147
D62V11, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          23                135
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          36                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"
D62V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4  53
  11P LOSS WILD-TYPE  12 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4   53
  11P LOSS WILD-TYPE   12  282
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 12
  NOT HISPANIC OR LATINO               53                282
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    43  26
  11Q LOSS WILD-TYPE 192 103
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                69                295 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                26                103 
$`11Q LOSS MUTATED`
TCGA-2Y-A9H6 TCGA-BC-A112 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-FV-A4ZP TCGA-KR-A7K7 
       11.74         5.03        90.28        26.83        81.73        31.27 
TCGA-UB-A7MF TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-3K-AAZ8 TCGA-5C-A9VG 
        7.04        23.80        24.89        49.84        13.02        10.78 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A217 
        0.66        14.76        27.91        37.32        46.78        45.93 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IK 
        4.24         3.35         9.86        11.93         9.99         8.61 
TCGA-CC-A7IL TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EF 
        9.14        79.73        83.57         2.60        90.71        12.95 
TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A73B TCGA-DD-AACO TCGA-DD-AACP 
       33.04        55.69        32.52         9.30        61.68        13.64 
TCGA-DD-AACV TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADO 
       50.33        44.22        22.09        40.08        40.47        14.89 
TCGA-DD-AADP TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEK 
       15.06        18.25        18.61         4.64        25.08        35.08 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A496 
        0.20        14.04         1.84         0.62        23.97         0.33 
TCGA-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        27.25 
TCGA-MI-A75G TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 
       22.95         0.72         0.49        19.33        19.04        36.10 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-YA-A8S7 
       27.88        16.44        13.55 

$`11Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BD-A3ER 
       83.24        38.40         8.61        69.57        17.98        36.66 
TCGA-DD-A3A8 TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG 
        0.36        18.87        21.17        21.83        18.90        23.64 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG 
        9.96        22.62         8.12         6.38        30.74        22.13 
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H 
       22.06         1.84        20.75         2.14        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT 
        0.76        10.32        29.52         0.69        40.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        41.79        80.28        27.88       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       56.91        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10R 
        8.55        10.59        17.10         1.51        48.99        10.13 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.38         1.12 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       44.42         0.26        22.36        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       44.81        13.45         0.66         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UE 
        3.39         3.32         9.96        10.36        11.41         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        7.13        21.34         9.83        12.00        13.12        12.56 
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-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
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-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       23.93        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        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-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       66.67        15.58        18.21        19.30        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH 
       20.98        19.99        23.74        15.72        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        90.48        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        60.99        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-A7XP 
       13.91        13.35         9.73         0.20        12.82        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41        13.35         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       19.59        11.93        14.40        60.89        19.10        27.88 
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-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-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       19.23        25.25        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.87        14.14        15.78        15.65        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       11.64        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        17.06        16.83        11.80        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M6 
       58.88        26.27        17.69        21.01         3.09         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       21.04        15.39        15.52        19.76         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY 
       18.28        33.86        30.41        22.78        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 

  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 
             18.25              20.12 
[1] "0.2 - 90.7 (18.2)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.2"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11Q LOSS MUTATED        28       15         0         20          1
  11Q LOSS WILD-TYPE     145       72         3         42          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q LOSS MUTATED            2        1         1         0
  11Q LOSS WILD-TYPE          5        1         0         2
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  28                145
  STAGE II                 15                 72
  STAGE III                 0                  3
  STAGE IIIA               20                 42
  STAGE IIIB                1                  8
  STAGE IIIC                2                  5
  STAGE IV                  1                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q LOSS MUTATED    30  18  23   1
  11Q LOSS WILD-TYPE 153  77  54  11
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               30                153
  T2               18                 77
  T3               23                 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"
D63V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    52   2
  11Q LOSS WILD-TYPE 202   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     52    2
  11Q LOSS WILD-TYPE  202    1
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               52                202
  1                2                  1
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    56   1
  11Q LOSS WILD-TYPE 210   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     56    1
  11Q LOSS WILD-TYPE  210    3
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               56                210
  1                1                  3
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    23  49
  11Q LOSS WILD-TYPE  95 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     23   49
  11Q LOSS WILD-TYPE   95  203
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               23                 95
  MALE                 49                203
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    64   1
  11Q LOSS WILD-TYPE 274   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     64    1
  11Q LOSS WILD-TYPE  274    8
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                64                274
  YES                1                  8
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11Q LOSS MUTATED                         2                       67
  11Q LOSS WILD-TYPE                       1                      293
                    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                         2                  1
  HEPATOCELLULAR CARCINOMA                       67                293
  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    62   6   0   4
  11Q LOSS WILD-TYPE 262  11   1  17
D63V10, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               62                262
  R1                6                 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
  11Q LOSS MUTATED                                  1    29
  11Q LOSS WILD-TYPE                                1   129
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           4    38
  11Q LOSS WILD-TYPE                        13   145
D63V11, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          29                129
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          38                145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     5  61
  11Q LOSS WILD-TYPE  11 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      5   61
  11Q LOSS WILD-TYPE   11  274
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 11
  NOT HISPANIC OR LATINO               61                274
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    40  23
  12P LOSS WILD-TYPE 195 106
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                63                301 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                23                106 
$`12P LOSS MUTATED`
TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-T1-A6J8 TCGA-ZP-A9D1 
       17.98        26.83         8.12         6.38         0.76         0.69 
TCGA-2Y-A9GS TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-BC-A217 TCGA-BD-A2L6 TCGA-CC-A1HT 
       23.80         8.55        13.02        45.93        44.81         3.32 
TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HV TCGA-DD-A119 
       11.93         8.94         8.61         9.14         9.17         7.33 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       45.11        49.15        33.04        13.64        55.69         5.62 
TCGA-DD-A3A1 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A73F 
        7.66        33.14        30.15        30.51        73.81        35.67 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACU TCGA-DD-AACY TCGA-DD-AAD5 
       71.80        15.42        42.81        51.52        47.67        44.22 
TCGA-DD-AAD8 TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEI 
       40.08         0.39        14.89        18.61        26.63        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVV TCGA-ED-A7XP TCGA-ED-A97K 
       35.08        90.48        72.39        80.71        13.15         0.20 
TCGA-EP-A2KC TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Z TCGA-G3-A7M6 TCGA-G3-AAV7 
        0.62         0.33        13.68        21.53        20.78        11.87 
TCGA-GJ-A6C0 TCGA-MI-A75G TCGA-MI-A75I TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A6M5 
        1.02        22.95        20.71        21.01         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7SK TCGA-UB-AA0U 
        0.30        15.52        10.75 

$`12P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25W 
       18.90        23.64         9.96        22.62        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       22.13        22.06         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE 
       12.72        24.56         7.04        10.32        29.52        40.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
       20.81        22.92         1.18        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-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
       23.38         1.12        44.42         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       12.72        18.48        13.45         0.66         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.19         3.39         4.24         3.35         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       10.36        11.41         9.99         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS 
       12.00        13.12        12.56         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-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI 
       66.31        19.79        75.65        11.47        12.95         6.02 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
       18.35        21.14        27.19        19.76        25.81        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       32.52        30.97        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-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05        22.78         1.45       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       11.41        75.65        76.41        55.40        12.53        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-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-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-AADC TCGA-DD-AADD 
       42.58        22.09        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       20.91        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH 
       19.99         4.64        23.74        15.72        25.08        25.78 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       89.69        82.62        59.93        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        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-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       12.82         0.20        14.04        13.41        13.35         1.84 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61        19.59        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        51.06        53.79        28.27        58.49        14.86 
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-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       20.42        17.10        14.70        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        11.64 
TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
        2.14        28.90         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
        9.57        16.67         7.53        10.85        58.88        26.27 
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-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
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-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        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 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.20               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             90.48             120.82 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             17.98              19.99 
[1] "0.2 - 90.5 (18.0)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.2"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED        24       18         1          9          4
  12P LOSS WILD-TYPE     149       69         2         53          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P LOSS MUTATED            2        2         1         0
  12P LOSS WILD-TYPE          5        0         0         2
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  24                149
  STAGE II                 18                 69
  STAGE III                 1                  2
  STAGE IIIA                9                 53
  STAGE IIIB                4                  5
  STAGE IIIC                2                  5
  STAGE IV                  2                  0
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED    28  23  13   2
  12P LOSS WILD-TYPE 155  72  64  10
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               28                155
  T2               23                 72
  T3               13                 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"
D64V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    42   3
  12P LOSS WILD-TYPE 212   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     42    3
  12P LOSS WILD-TYPE  212    0
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               42                212
  1                3                  0
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    50   2
  12P LOSS WILD-TYPE 216   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     50    2
  12P LOSS WILD-TYPE  216    2
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               50                216
  1                2                  2
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    20  46
  12P LOSS WILD-TYPE  98 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     20   46
  12P LOSS WILD-TYPE   98  206
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               20                 98
  MALE                 46                206
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    59   0
  12P LOSS WILD-TYPE 279   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     59    0
  12P LOSS WILD-TYPE  279    9
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                59                279
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12P LOSS MUTATED                         1                       64
  12P LOSS WILD-TYPE                       2                      296
                    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                         1                  2
  HEPATOCELLULAR CARCINOMA                       64                296
  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    54   5   1   4
  12P LOSS WILD-TYPE 270  12   0  17
D64V10, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               54                270
  R1                5                 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    31
  12P LOSS WILD-TYPE                                2   127
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           4    29
  12P LOSS WILD-TYPE                        13   154
D64V11, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          31                127
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          29                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"
D64V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3  59
  12P LOSS WILD-TYPE  13 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3   59
  12P LOSS WILD-TYPE   13  276
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               59                276
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    19  14
  12Q LOSS WILD-TYPE 216 115
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                33                331 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                14                115 
$`12Q LOSS MUTATED`
TCGA-DD-A4NI TCGA-FV-A3I1 TCGA-ZP-A9D1 TCGA-2Y-A9GS TCGA-3K-AAZ8 TCGA-BC-A217 
       26.83         8.12         0.69        23.80        13.02        45.93 
TCGA-CC-A1HT TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IL TCGA-CC-A8HV TCGA-DD-A119 
        3.32        11.93         8.94         9.14         9.17         7.33 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A4NO 
       45.11        49.15        13.64        55.69         5.62        73.81 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACU TCGA-DD-AAD8 TCGA-DD-AAE3 
       71.80        15.42        42.81        51.52        40.08        18.61 
TCGA-DD-AAEK TCGA-DD-AAVU TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A496 TCGA-G3-A25Z 
       35.08        72.39         0.20         0.62         0.33        21.53 
TCGA-MI-A75G TCGA-RC-A6M4 TCGA-RC-A6M5 
       22.95         0.72         0.49 

$`12Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        90.28        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 
       21.83        18.90        23.64         9.96        22.62         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       10.32        29.52        40.80        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       80.28        24.89        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       49.84        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55        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-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       44.42         0.26        22.36        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       44.81        13.45         0.66         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.35         9.86         9.96        10.36 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.41         9.99         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS 
       13.12        12.56         8.61         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-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI 
       66.31        19.79        75.65        11.47        12.95         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 
       33.04        18.35        21.14        27.19        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78        30.61        33.14        32.52        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-AACF 
       11.41        75.65        76.41        55.40        12.53        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-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-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-AADA TCGA-DD-AADB 
       21.63        42.58        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-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-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.25        18.15        20.98        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       90.48        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        60.99 
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-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       19.59        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       27.88        12.03         0.03         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        58.49        14.86        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-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-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M6 
       58.88        26.27        17.69        21.01         3.09         0.30 
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-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
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-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        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 

  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 
             15.42              19.99 
[1] "0.2 - 73.8 (15.4)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.4"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED        12       10         1          6          2
  12Q LOSS WILD-TYPE     161       77         2         56          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q LOSS MUTATED            0        2         1         0
  12Q LOSS WILD-TYPE          7        0         0         2
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  12                161
  STAGE II                 10                 77
  STAGE III                 1                  2
  STAGE IIIA                6                 56
  STAGE IIIB                2                  7
  STAGE IIIC                0                  7
  STAGE IV                  2                  0
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED    14  12   9   1
  12Q LOSS WILD-TYPE 169  83  68  11
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               14                169
  T2               12                 83
  T3                9                 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"
D65V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    24   1
  12Q LOSS WILD-TYPE 230   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     24    1
  12Q LOSS WILD-TYPE  230    2
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               24                230
  1                1                  2
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    27   2
  12Q LOSS WILD-TYPE 239   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     27    2
  12Q LOSS WILD-TYPE  239    2
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               27                239
  1                2                  2
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    11  25
  12Q LOSS WILD-TYPE 107 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     11   25
  12Q LOSS WILD-TYPE  107  227
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               11                107
  MALE                 25                227
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    31   0
  12Q LOSS WILD-TYPE 307   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     31    0
  12Q LOSS WILD-TYPE  307    9
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                31                307
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12Q LOSS MUTATED                         1                       34
  12Q LOSS WILD-TYPE                       2                      326
                    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                         1                  2
  HEPATOCELLULAR CARCINOMA                       34                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
  12Q LOSS MUTATED    31   1   1   2
  12Q LOSS WILD-TYPE 293  16   0  19
D65V10, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               31                293
  R1                1                 16
  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    19
  12Q LOSS WILD-TYPE                                2   139
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           3    14
  12Q LOSS WILD-TYPE                        14   169
D65V11, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          19                139
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          14                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"
D65V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2  32
  12Q LOSS WILD-TYPE  14 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   32
  12Q LOSS WILD-TYPE   14  303
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               32                303
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    73  46
  13Q LOSS WILD-TYPE 162  83
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               119                245 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                46                 83 
$`13Q LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-FV-A3R2 TCGA-ZS-A9CE 
        5.03        17.98        21.83        23.64         6.38        40.80 
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-A217 
       10.78        10.59        37.32        10.13        27.52        45.93 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       22.36        14.60        18.48         0.66         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        3.19         3.39         3.35         9.86         9.96        11.93 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HV 
       11.41         8.94        12.56         8.61         9.14         9.17 
TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        6.94        79.73        83.57        53.33       113.00         2.60 
TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y 
       21.76        12.95         6.02        18.35        55.69         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NN 
       25.81       102.74        30.61        33.14        30.15        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACG 
       73.81        12.26        35.67       114.35        13.48        15.42 
TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS 
       53.19         3.52        58.16        42.81        13.64        59.31 
TCGA-DD-AAD1 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       18.54        40.08        13.97        40.47         3.78        35.67 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AAE0 TCGA-DD-AAED 
       34.49         0.39        14.89        66.67        18.25        25.08 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PX 
       35.08        89.69        80.71        29.92        26.93         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A3RK TCGA-G3-A25S TCGA-G3-A25T 
        0.20        14.04        13.15        11.93        13.68        51.06 
TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-AAV4 
       58.49        25.64        17.10        14.70        20.78         0.89 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-MI-A75G 
       11.87        28.90         2.20        17.06        27.25        22.95 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A6M5 
       20.71        10.85        26.27        21.01         0.72         0.49 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-AA0U TCGA-WJ-A86L 
       19.04        15.39        15.52        27.88        10.75        11.34 
TCGA-XR-A8TD TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZS-A9CG 
       33.86        22.78        13.55        25.71        11.21 

$`13Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAEA 
        0.36        90.28        26.83        18.87        21.17        18.90 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG 
        9.96        22.62         8.12        81.73        30.74        22.13 
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG 
       22.06         1.84        20.75         2.14        31.27        12.72 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 
       24.56         0.76         7.04        10.32        29.52         0.69 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        63.75        41.79        80.28        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       40.41        49.84        47.74        22.92         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-A10U 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-A216 TCGA-BC-A3KF TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5263 
       44.42         0.26        12.72        44.81        13.45         4.24 
TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
        3.32        10.36         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-A4NB TCGA-DD-A4NF 
       17.59        20.12       107.11        13.78        32.52        30.97 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       30.51        39.78        56.25       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACO 
       71.80        12.00         6.41        69.11         0.30        61.68 
TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       14.20        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
       47.67         5.62         4.50        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADJ 
       22.09        40.54        40.83        39.52        37.64        35.05 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
       20.91        29.52        15.06        14.33        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       19.30        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
        4.64        23.74        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 
       90.48        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        60.99        53.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E 
       28.08        13.91        13.35         9.73        12.82        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       19.59         0.62        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U 
       27.88        12.03         0.03         0.33         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       28.27        14.86        21.53         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       25.25        22.95        20.42        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 
       15.65        11.80        12.23        13.55        11.64         2.14 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 
        1.02         2.99        37.71        16.83        11.80        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-NI-A4U2 
       13.97        12.03         9.57        16.67         7.53        58.88 
TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RG-A7D4 
       17.69         3.09         0.30        21.04        19.33        36.10 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       19.76        16.44         1.71        15.98         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9CZ 
       20.22        24.85        18.28        30.41        35.77        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       35.87        25.15        12.99        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              20.22 
[1] "0.2 - 114.3 (18.2)" "0.0 - 120.8 (20.2)"
[1] "hr=" "1.2"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED        47       35         1         19          5
  13Q LOSS WILD-TYPE     126       52         2         43          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q LOSS MUTATED            4        0         1         2
  13Q LOSS WILD-TYPE          3        2         0         0
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  47                126
  STAGE II                 35                 52
  STAGE III                 1                  2
  STAGE IIIA               19                 43
  STAGE IIIB                5                  4
  STAGE IIIC                4                  3
  STAGE IV                  0                  2
  STAGE IVA                 1                  0
  STAGE IVB                 2                  0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED    50  39  25   8
  13Q LOSS WILD-TYPE 133  56  52   4
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               50                133
  T2               39                 56
  T3               25                 52
  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"
D66V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    86   2
  13Q LOSS WILD-TYPE 168   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     86    2
  13Q LOSS WILD-TYPE  168    1
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               86                168
  1                2                  1
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    89   2
  13Q LOSS WILD-TYPE 177   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     89    2
  13Q LOSS WILD-TYPE  177    2
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               89                177
  1                2                  2
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    46  76
  13Q LOSS WILD-TYPE  72 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     46   76
  13Q LOSS WILD-TYPE   72  176
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               46                 72
  MALE                 76                176
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   111   2
  13Q LOSS WILD-TYPE 227   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    111    2
  13Q LOSS WILD-TYPE  227    7
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               111                227
  YES                2                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  13Q LOSS MUTATED                         2                      117
  13Q LOSS WILD-TYPE                       1                      243
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  13Q LOSS MUTATED                                  3
  13Q LOSS WILD-TYPE                                4
D66V9, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  1
  HEPATOCELLULAR CARCINOMA                      117                243
  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
  13Q LOSS MUTATED   101   8   0  10
  13Q LOSS WILD-TYPE 223   9   1  11
D66V10, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0              101                223
  R1                8                  9
  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                                  1    56
  13Q LOSS WILD-TYPE                                1   102
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           5    60
  13Q LOSS WILD-TYPE                        12   123
D66V11, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          56                102
  BLACK OR AFRICAN AMERICAN                       5                 12
  WHITE                                          60                123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     5 111
  13Q LOSS WILD-TYPE  11 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5  111
  13Q LOSS WILD-TYPE   11  224
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 11
  NOT HISPANIC OR LATINO              111                224
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    61  45
  14Q LOSS WILD-TYPE 174  84
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               106                258 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                45                 84 
$`14Q LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAEG TCGA-FV-A4ZP TCGA-G3-A7M9 
        5.03        26.83        18.87        23.64        81.73         1.84 
TCGA-KR-A7K7 TCGA-2Y-A9GS TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H3 
       31.27        23.80        80.28        24.89        40.41        49.84 
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A217 
       10.78         0.66        37.32        10.13        27.52        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-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       90.71        45.11         6.02        33.04        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NH 
        5.62         7.66        13.78        30.61        32.52        30.15 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-AA3A TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACN 
       73.81        12.26        13.48        71.80        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-AADW TCGA-DD-AAE0 TCGA-DD-AAE6 TCGA-DD-AAEE TCGA-DD-AAVU 
       66.67        19.30        18.25         4.64        26.63        72.39 
TCGA-DD-AAVV TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E 
       80.71        53.69        29.92         0.20         0.20        13.41 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A3RK TCGA-G3-A25S TCGA-G3-A25X 
        1.84         0.20        19.59        11.93        13.68        58.49 
TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-AAV1 TCGA-G3-AAV7 TCGA-K7-A5RG TCGA-NI-A8LF 
       25.64        17.10        11.80        11.87        17.06        26.27 
TCGA-RC-A6M5 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC 
        0.49        19.04        15.39        15.52        36.10        16.44 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-ZP-A9D2 
        0.99        12.99        20.22        25.15 

$`14Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
       36.66         0.36        90.28        21.17        21.83        18.90 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG 
        9.96        22.62         8.12         6.38        30.74        22.13 
TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       22.06        20.75         2.14        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT 
        7.04        10.32        29.52         0.69        40.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H4 
       63.75        41.79        27.88       120.82        56.91        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
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-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52         2.99        25.32        23.38         1.12 
TCGA-BC-A216 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       44.42        14.60        12.72        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A5UC TCGA-CC-A5UD 
        0.66         3.39         4.24         9.86        11.41         9.99 
TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 
       21.34        12.00         9.14         6.94         8.15        37.78 
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-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EK 
       19.79        75.65        11.47        12.95        49.15        18.35 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        27.19        19.76        25.81        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NJ 
       20.12       102.74       107.11        33.14        30.97        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       35.67       114.35         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-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.35        50.33        46.82         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC 
       18.54        21.63        42.58        40.08        40.54        13.97 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADP 
       39.52        37.64        35.67        35.05        34.49        15.06 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
       14.33        15.58        18.21        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH 
       18.61        19.99        23.74        15.72        25.08        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       60.99        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
       12.82        14.04        13.15        13.35        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       20.61         0.62        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T 
       27.88        12.03         0.03         0.33         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ 
       53.79        28.27        14.86        21.53         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M6 
       19.23        25.25        22.95        20.42        14.70        20.78 
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-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89        11.64         2.14        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
        2.99        37.71        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        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-A6M4 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-UB-A7MA TCGA-UB-A7MB 
        0.72         0.30        21.04        19.33        27.88        19.76 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WX-AA46 TCGA-WX-AA47 
        1.71        15.98        10.75        11.34        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       23.21        35.87        12.99        45.57        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 
             17.08              20.66 
[1] "0.2 - 113.0 (17.1)" "0.0 - 120.8 (20.7)"
[1] "hr=" "1.4"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED        40       30         0         22          4
  14Q LOSS WILD-TYPE     133       57         3         40          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q LOSS MUTATED            3        1         1         1
  14Q LOSS WILD-TYPE          4        1         0         1
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  40                133
  STAGE II                 30                 57
  STAGE III                 0                  3
  STAGE IIIA               22                 40
  STAGE IIIB                4                  5
  STAGE IIIC                3                  4
  STAGE IV                  1                  1
  STAGE IVA                 1                  0
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q LOSS MUTATED    42  34  28   5
  14Q LOSS WILD-TYPE 141  61  49   7
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               42                141
  T2               34                 61
  T3               28                 49
  T4                5                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    78   2
  14Q LOSS WILD-TYPE 176   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     78    2
  14Q LOSS WILD-TYPE  176    1
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               78                176
  1                2                  1
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    87   2
  14Q LOSS WILD-TYPE 179   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     87    2
  14Q LOSS WILD-TYPE  179    2
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               87                179
  1                2                  2
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    31  78
  14Q LOSS WILD-TYPE  87 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     31   78
  14Q LOSS WILD-TYPE   87  174
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               31                 87
  MALE                 78                174
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   100   2
  14Q LOSS WILD-TYPE 238   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    100    2
  14Q LOSS WILD-TYPE  238    7
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               100                238
  YES                2                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  14Q LOSS MUTATED                         2                      104
  14Q LOSS WILD-TYPE                       1                      256
                    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                         2                  1
  HEPATOCELLULAR CARCINOMA                      104                256
  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    94   5   0   8
  14Q LOSS WILD-TYPE 230  12   1  13
D67V10, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               94                230
  R1                5                 12
  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    59
  14Q LOSS WILD-TYPE                                2    99
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           4    44
  14Q LOSS WILD-TYPE                        13   139
D67V11, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          59                 99
  BLACK OR AFRICAN AMERICAN                       4                 13
  WHITE                                          44                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"
D67V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     5  97
  14Q LOSS WILD-TYPE  11 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5   97
  14Q LOSS WILD-TYPE   11  238
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 11
  NOT HISPANIC OR LATINO               97                238
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    33  31
  15Q LOSS WILD-TYPE 202  98
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                64                300 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                31                 98 
$`15Q LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-2Y-A9H8 
        5.03        17.98        81.73         1.84        31.27        20.81 
TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5264 TCGA-CC-A3MA 
       13.02        10.59        14.60         4.24         3.35         9.96 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       11.41         9.99         9.83        13.12        12.56         8.61 
TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11A 
        9.17         8.15        79.73        37.78        83.57         2.60 
TCGA-DD-A1E9 TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 
       90.71         6.02        33.04        13.64         5.62       102.74 
TCGA-DD-A4NA TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACG TCGA-DD-AACL 
       33.14        12.26         9.30         0.53        15.42         3.52 
TCGA-DD-AADB TCGA-DD-AADK TCGA-DD-AADO TCGA-DD-AAE1 TCGA-DD-AAVQ TCGA-DD-AAVV 
       40.83        34.49        14.89        18.15        89.69        80.71 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KB 
       29.92         9.73         0.20         0.20        13.41        19.59 
TCGA-FV-A496 TCGA-G3-A25Z TCGA-G3-A5SM TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 
        0.33        21.53        17.10        11.80         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-RC-A6M4 TCGA-RG-A7D4 
       11.87        28.90        17.06        27.25         0.72        36.10 
TCGA-UB-A7MA TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CF 
       27.88         0.99        13.55        79.30 

$`15Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
        0.36        90.28        26.83        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       18.90        23.64         9.96        22.62         8.12         6.38 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG 
       30.74        22.13        22.06        20.75         2.14        12.72 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 
       24.56         0.76         7.04        10.32        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        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-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG 
       47.74        18.25        22.92         1.18         8.55        10.78 
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-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        12.72        18.48        44.81        13.45         0.66 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.19         3.39         4.24         3.32         9.86 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH 
       10.36        11.93         8.94         7.13        21.34        12.00 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A116 TCGA-DD-A118 
        9.14         4.60        11.31         6.94        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         0.46        21.76        51.29        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        21.14        27.19        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.61        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      114.35        13.48        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        71.80        12.00         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        0.30        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD 
       44.22        22.09        40.08        40.54        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADL 
       39.52         3.78        37.64        35.67        35.05        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 
       18.21        19.30        18.25        18.25        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        35.08        90.48        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        60.99        53.69        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 
       13.35        12.82        14.04        13.15        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK 
        0.20        18.74        19.99        20.61         0.62        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-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       58.49        14.86        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       25.25        22.95        20.42        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 
       14.14        15.78        15.65        12.23        13.55        11.64 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.20         2.99        37.71        16.83        11.80 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
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-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
       21.01         3.09         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       19.04        15.39        15.52        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        10.75        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY 
       18.28        33.86        30.41        22.78        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.21        35.87        25.15        12.99        45.57        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 
            13.265             20.945 
[1] "0.2 - 102.7 (13.3)" "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         16          2
  15Q LOSS WILD-TYPE     153       65         2         46          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q LOSS MUTATED            3        0         0         0
  15Q LOSS WILD-TYPE          4        2         1         2
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  20                153
  STAGE II                 22                 65
  STAGE III                 1                  2
  STAGE IIIA               16                 46
  STAGE IIIB                2                  7
  STAGE IIIC                3                  4
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED    22  23  21   1
  15Q LOSS WILD-TYPE 161  72  56  11
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               22                161
  T2               23                 72
  T3               21                 56
  T4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    45   2
  15Q LOSS WILD-TYPE 209   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     45    2
  15Q LOSS WILD-TYPE  209    1
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               45                209
  1                2                  1
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    56   0
  15Q LOSS WILD-TYPE 210   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     56    0
  15Q LOSS WILD-TYPE  210    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               56                210
  1                0                  4
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    21  46
  15Q LOSS WILD-TYPE  97 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     21   46
  15Q LOSS WILD-TYPE   97  206
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               21                 97
  MALE                 46                206
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    59   1
  15Q LOSS WILD-TYPE 279   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     59    1
  15Q LOSS WILD-TYPE  279    8
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                59                279
  YES                1                  8
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  15Q LOSS MUTATED                         0                       65
  15Q LOSS WILD-TYPE                       3                      295
                    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                  3
  HEPATOCELLULAR CARCINOMA                       65                295
  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    58   4   0   5
  15Q LOSS WILD-TYPE 266  13   1  16
D68V10, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               58                266
  R1                4                 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
  15Q LOSS MUTATED                                  1    31
  15Q LOSS WILD-TYPE                                1   127
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           6    29
  15Q LOSS WILD-TYPE                        11   154
D68V11, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          31                127
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          29                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"
D68V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3  60
  15Q LOSS WILD-TYPE  13 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3   60
  15Q LOSS WILD-TYPE   13  275
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               60                275
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    63  42
  16P LOSS WILD-TYPE 172  87
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               105                259 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                42                 87 
$`16P LOSS MUTATED`
TCGA-2Y-A9H7 TCGA-BC-A5W4 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE8 
       38.40        17.98         0.36        90.28        26.83        21.83 
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-A7MF 
       22.62         6.38         1.84        31.27         0.76         7.04 
TCGA-ZP-A9D1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-BC-A217 TCGA-BC-A69H 
        0.69        56.91        49.84        20.81        45.93        14.60 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45         0.66         4.24         2.86         3.19         3.39 
TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE 
        3.35         9.86        10.36        11.93        11.41         8.94 
TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS 
        7.13        13.12        12.56         4.60         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
        8.15        37.78         0.46        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NN 
       33.04         5.62        19.76        30.61        30.15        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL 
       73.81        12.26         9.30        55.40        15.42         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACZ 
       58.16        42.81        13.64        51.52        46.82         5.62 
TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADL 
       42.58        40.54        40.83        35.67        35.05        20.91 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       14.89        15.06        66.67        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVU 
       18.15         4.64        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-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A25X 
        1.84        19.59        60.89        23.97        27.88        58.49 
TCGA-G3-A25Y TCGA-G3-A7M5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-MI-A75G TCGA-MI-A75I 
       14.86        14.70         2.14        11.87        22.95        20.71 
TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-WQ-A9G7 
        3.09        19.33        15.39        36.10        27.88         0.99 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CG 
       22.78        13.55        11.21 

$`16P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BD-A3ER 
       83.24        11.74         8.61        69.57         5.03        36.66 
TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       18.87        21.17        18.90        23.64         9.96         8.12 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 
       81.73        30.74        22.13        22.06        20.75         2.14 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS 
       12.72        24.56        10.32        29.52        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
      120.82        40.41        47.74        18.25        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55        13.02        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-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO 
        1.12        44.42         0.26        22.36        12.72        18.48 
TCGA-BD-A2L6 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A5UD TCGA-CC-A7IF 
       44.81         4.24         3.32         9.96         9.99        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-DD-A113 
        9.83        12.00         8.61         9.14        11.31        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
       83.57        53.33       113.00         7.33         2.60        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       11.47        45.11        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        13.78        33.14        32.52        30.97 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       30.51        39.78        56.25       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        71.80        12.00         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV 
        0.30        61.68        14.20        59.31        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-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.21        20.98        18.61        19.99        23.74        15.72 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       26.63        25.78        50.33        90.48        89.69        82.62 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW1 
       80.71        76.18        56.48        64.77        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A7PX 
       60.99        53.69        29.92        26.93        13.91         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A12J 
        0.20        14.04        13.15        13.41         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       19.99        20.61         0.62        11.93        14.40        19.10 
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-A25U TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       53.79        28.27        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-A7M6 
       19.23        25.25        22.95        20.42        17.10        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-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       13.55         0.89        11.64        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 
       29.79        13.97        12.03         9.57        16.67         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A6M4 
       10.85        58.88        26.27        17.69        21.01         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MB 
        0.49         0.30        21.04        19.04        15.52        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B 
       16.44         1.71        15.98        10.75        11.34        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-ZP-A9CV 
       20.22        24.85        18.28        33.86        30.41        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-A9CF 
       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 
             15.42              20.78 
[1] "0.4 - 90.3 (15.4)"  "0.0 - 120.8 (20.8)"
[1] "hr=" "1.5"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P LOSS MUTATED        43       31         1         20          3
  16P LOSS WILD-TYPE     130       56         2         42          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P LOSS MUTATED            3        1         0         1
  16P LOSS WILD-TYPE          4        1         1         1
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  43                130
  STAGE II                 31                 56
  STAGE III                 1                  2
  STAGE IIIA               20                 42
  STAGE IIIB                3                  6
  STAGE IIIC                3                  4
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED    47  33  24   4
  16P LOSS WILD-TYPE 136  62  53   8
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               47                136
  T2               33                 62
  T3               24                 53
  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   1
  16P LOSS WILD-TYPE 173   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     81    1
  16P LOSS WILD-TYPE  173    2
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               81                173
  1                1                  2
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    87   2
  16P LOSS WILD-TYPE 179   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     87    2
  16P LOSS WILD-TYPE  179    2
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               87                179
  1                2                  2
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    39  69
  16P LOSS WILD-TYPE  79 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     39   69
  16P LOSS WILD-TYPE   79  183
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               39                 79
  MALE                 69                183
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   100   0
  16P LOSS WILD-TYPE 238   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    100    0
  16P LOSS WILD-TYPE  238    9
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO               100                238
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16P LOSS MUTATED                         0                      106
  16P LOSS WILD-TYPE                       3                      254
                    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                  3
  HEPATOCELLULAR CARCINOMA                      106                254
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    95   2   0  10
  16P LOSS WILD-TYPE 229  15   1  11
D69V10, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               95                229
  R1                2                 15
  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    61
  16P LOSS WILD-TYPE                                2    97
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           6    40
  16P LOSS WILD-TYPE                        11   143
D69V11, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          61                 97
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          40                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"
D69V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     6  99
  16P LOSS WILD-TYPE  10 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      6   99
  16P LOSS WILD-TYPE   10  236
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 10
  NOT HISPANIC OR LATINO               99                236
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    87  55
  16Q LOSS WILD-TYPE 148  74
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               142                222 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                55                 74 
$`16Q LOSS MUTATED`
TCGA-2Y-A9H7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE8 TCGA-ES-A2HS 
       38.40         0.36        90.28        26.83        21.83        22.62 
TCGA-FV-A3R2 TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-ZP-A9D1 
        6.38         1.84        31.27         0.76         7.04         0.69 
TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA 
       24.89        56.91        49.84        18.25        20.81         1.18 
TCGA-5C-AAPD TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        0.66        46.78         2.99        44.42        45.93        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       14.60        18.48        13.45         0.66         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.19         4.24         3.35        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A8HT 
        9.99         8.94         7.13        21.34         9.83         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-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       53.33         2.60         0.46        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NN 
       33.04         5.62        19.76        30.61        30.15        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG 
       73.81        12.26         9.30        55.40        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41        53.19         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACZ 
       13.64        14.20        59.31        51.52        46.82         5.62 
TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI TCGA-DD-AADJ 
       18.54        42.58        40.54        40.83        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR 
       34.49        20.91         0.39        14.89        15.06        66.67 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAED 
       19.30        18.25        18.25        18.15         4.64        25.08 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       25.78        35.08        89.69        59.93        72.39        76.18 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       62.47        66.25        29.92        28.08        13.35         9.73 
TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A2QQ 
       12.82        13.35         1.84        19.59        60.89        23.97 
TCGA-FV-A3I0 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
       27.88        13.68        53.79        58.49        14.86        25.64 
TCGA-G3-A5SI TCGA-G3-A7M5 TCGA-G3-AAUZ TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-MI-A75G 
       25.25        14.70        15.78         2.14        11.87        22.95 
TCGA-MI-A75I TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       20.71        17.69         3.09        19.33        19.04        15.39 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       36.10        27.88        19.76        10.75        11.34         0.99 
TCGA-XR-A8TD TCGA-XR-A8TF TCGA-ZP-A9CZ TCGA-ZS-A9CG 
       33.86        22.78        23.21        11.21 

$`16Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL 
       36.66        18.87        21.17        18.90        23.64         9.96 
TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
        8.12        81.73        30.74        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE 
        2.14        12.72        24.56        10.32        29.52        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       23.80        53.39        63.75        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 
      120.82        40.41        47.74        22.92         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.78        10.59        17.10        14.76         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       27.91        37.32        10.13        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A69I TCGA-BD-A2L6 TCGA-CC-5262 
       23.38         1.12         0.26        12.72        44.81         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        3.32         9.86         9.96        12.00        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C 
        8.61         9.14        83.57       113.00         7.33        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       11.47        45.11        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        13.78        33.14        32.52        30.97 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       30.51        39.78        56.25       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACT TCGA-DD-AACV 
       12.53        71.80        69.11         0.30        51.35        50.33 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.59        47.67         4.50        21.63        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.08        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE2 TCGA-DD-AAE3 
       29.52        14.33        15.58        18.21        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVP 
       19.99        23.74        15.72        26.63        50.33        90.48 
TCGA-DD-AAVR TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 
       82.62        80.71        56.48        64.77        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO 
       53.69        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-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 
        0.62        11.93        14.40        19.10        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CI 
        0.33         0.39        51.06        28.27        21.53         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 
       19.53        19.23        22.95        20.42        17.10        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       11.87        14.14        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        0.89        11.64        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO 
       13.97        12.03         9.57        16.67         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       58.88        26.27        21.01         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WQ-AB4B 
       21.04        15.52        16.44         1.71        15.98        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        30.41        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       25.71        35.87        25.15        12.99        45.57        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 
            18.790             20.515 
[1] "0.4 - 90.3 (18.8)"  "0.0 - 120.8 (20.5)"
[1] "hr=" "1.4"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED        59       45         1         23          4
  16Q LOSS WILD-TYPE     114       42         2         39          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q LOSS MUTATED            3        1         0         1
  16Q LOSS WILD-TYPE          4        1         1         1
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  59                114
  STAGE II                 45                 42
  STAGE III                 1                  2
  STAGE IIIA               23                 39
  STAGE IIIB                4                  5
  STAGE IIIC                3                  4
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED    64  47  29   5
  16Q LOSS WILD-TYPE 119  48  48   7
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               64                119
  T2               47                 48
  T3               29                 48
  T4                5                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   109   1
  16Q LOSS WILD-TYPE 145   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    109    1
  16Q LOSS WILD-TYPE  145    2
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              109                145
  1                1                  2
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   115   2
  16Q LOSS WILD-TYPE 151   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    115    2
  16Q LOSS WILD-TYPE  151    2
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              115                151
  1                2                  2
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    51  94
  16Q LOSS WILD-TYPE  67 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     51   94
  16Q LOSS WILD-TYPE   67  158
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               51                 67
  MALE                 94                158
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   134   2
  16Q LOSS WILD-TYPE 204   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    134    2
  16Q LOSS WILD-TYPE  204    7
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               134                204
  YES                2                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16Q LOSS MUTATED                         0                      142
  16Q LOSS WILD-TYPE                       3                      218
                    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                  3
  HEPATOCELLULAR CARCINOMA                      142                218
  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   128   6   0  11
  16Q LOSS WILD-TYPE 196  11   1  10
D70V10, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0              128                196
  R1                6                 11
  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                                2    74
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           7    51
  16Q LOSS WILD-TYPE                        10   132
D70V11, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          84                 74
  BLACK OR AFRICAN AMERICAN                       7                 10
  WHITE                                          51                132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     8 133
  16Q LOSS WILD-TYPE   8 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8  133
  16Q LOSS WILD-TYPE    8  202
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  8
  NOT HISPANIC OR LATINO              133                202
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   106  75
  17P LOSS WILD-TYPE 129  54
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               181                183 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                75                 54 
$`17P LOSS MUTATED`
TCGA-2Y-A9GV TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV 
       83.24        69.57         5.03        17.98        26.83        18.87 
TCGA-DD-AAEA TCGA-G3-A7M9 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-UB-A7MF 
       18.90         1.84         2.14        12.72         0.76         7.04 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GY 
       29.52         0.69        40.80        23.80        53.39        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       27.88       120.82        56.91        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-5C-AAPD TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        1.18         0.66         1.51        48.99        27.91        10.13 
TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       27.52        23.38         1.12        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 
       14.60        18.48        44.81        13.45         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MB 
        3.19         3.39         4.24         3.35         3.32        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7II 
       11.93        11.41         9.99         8.94        21.34        13.12 
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-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
       83.57        53.33       113.00         7.33         2.60        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       51.29        79.40        66.31        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A3 
       33.04        18.35        13.64         5.62        25.81        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NJ 
       20.12       102.74        33.14        32.52        30.15        30.51 
TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE 
       12.26         9.30         1.45        75.65        55.40        71.80 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ 
       15.42         6.41        69.11         3.52        58.16        14.20 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
        5.59         5.62        18.54        42.58        22.09        40.08 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL 
       40.83        13.97        39.52         3.78        37.64        20.91 
TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 
       29.52        66.67        19.30        18.25        18.25        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK 
       19.99         4.64        15.72        26.63        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAW1 
       90.48        89.69        82.62        72.39        80.71        65.39 
TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K 
       29.92         0.20         0.20        13.41         1.84         0.20 
TCGA-EP-A2KC TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 
        0.62        60.89        23.97        19.10        27.88         0.03 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       13.68        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV1 
       20.42        17.10        14.70        20.78        15.78        11.80 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5N0 
        0.89        11.64        11.87        28.90         1.02        37.71 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
       11.80        27.25        16.67        22.95        20.71        58.88 
TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB 
       17.69         3.09         0.72         0.49         0.30        19.33 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       15.52        36.10        19.76        16.44         1.71        15.98 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-XR-A8TD TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       11.34        12.99        33.86        13.55        25.15        12.99 
TCGA-ZS-A9CF 
       79.30 

$`17P LOSS WILD-TYPE`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND 
       11.74        38.40         8.61        36.66         0.36        90.28 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.17        21.83        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
        6.38        81.73        30.74        22.13        22.06        20.75 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-UB-AA0V TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       31.27        24.56        10.32        63.75        41.79        80.28 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       40.41        49.84        47.74         8.55        13.02        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-BW-A5NO TCGA-CC-A3M9 
        2.99        25.32        44.42        12.72         0.66         9.86 
TCGA-CC-A3MA TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A9FW 
        9.96         7.13         9.83        12.00        12.56         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED 
       79.73        37.78         0.46        90.71        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       11.47        12.95        21.14        27.19        55.69        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NF 
        7.66        70.06       107.11        13.78        30.61        30.97 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR 
       39.78        56.25        29.56        73.81       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       80.75        78.84        23.93        23.05        22.78        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD 
      114.35        13.48         0.53        11.41        76.41        12.53 
TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       12.00        53.19         0.30        42.81        61.68        13.64 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY 
       59.31        51.35        51.52        50.33        46.82        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADI 
        4.50        21.63        44.22        40.54        40.47        35.67 
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-AADS TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAED 
       15.58        18.21        18.15        18.61        23.74        25.08 
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        60.99        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-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61        19.59        11.93        14.40 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CI 
       12.03         0.33         0.39        51.06        58.49         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M7 TCGA-G3-A7M8 
       19.53        19.23        25.25        22.95        11.87        14.14 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       15.65        12.23        13.55         2.14         2.20         2.99 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       17.06        16.83        29.79        13.97        12.03         9.57 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF 
        7.53        10.85        26.27        21.01        21.04        19.04 
TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 
       15.39        27.88        10.75         0.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       18.28        30.41        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       35.87        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 
             18.48              21.14 
[1] "0.0 - 120.8 (18.5)" "0.3 - 114.3 (21.1)"
[1] "hr=" "1.6"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED        70       50         2         34          4
  17P LOSS WILD-TYPE     103       37         1         28          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P LOSS MUTATED            7        2         1         1
  17P LOSS WILD-TYPE          0        0         0         1
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  70                103
  STAGE II                 50                 37
  STAGE III                 2                  1
  STAGE IIIA               34                 28
  STAGE IIIB                4                  5
  STAGE IIIC                7                  0
  STAGE IV                  2                  0
  STAGE IVA                 1                  0
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P LOSS MUTATED    77  57  42   8
  17P LOSS WILD-TYPE 106  38  35   4
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               77                106
  T2               57                 38
  T3               42                 35
  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   127   3
  17P LOSS WILD-TYPE 127   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    127    3
  17P LOSS WILD-TYPE  127    0
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              127                127
  1                3                  0
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   137   3
  17P LOSS WILD-TYPE 129   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    137    3
  17P LOSS WILD-TYPE  129    1
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              137                129
  1                3                  1
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    60 125
  17P LOSS WILD-TYPE  58 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     60  125
  17P LOSS WILD-TYPE   58  127
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               60                 58
  MALE                125                127
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   168   4
  17P LOSS WILD-TYPE 170   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    168    4
  17P LOSS WILD-TYPE  170    5
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               168                170
  YES                4                  5
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17P LOSS MUTATED                         2                      178
  17P LOSS WILD-TYPE                       1                      182
                    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                         2                  1
  HEPATOCELLULAR CARCINOMA                      178                182
  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   159   9   1  14
  17P LOSS WILD-TYPE 165   8   0   7
D71V10, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              159                165
  R1                9                  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                                  1    85
  17P LOSS WILD-TYPE                                1    73
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           9    86
  17P LOSS WILD-TYPE                         8    97
D71V11, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          85                 73
  BLACK OR AFRICAN AMERICAN                       9                  8
  WHITE                                          86                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    10 165
  17P LOSS WILD-TYPE   6 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     10  165
  17P LOSS WILD-TYPE    6  170
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                   10                  6
  NOT HISPANIC OR LATINO              165                170
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    22  15
  17Q LOSS WILD-TYPE 213 114
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                37                327 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                15                114 
$`17Q LOSS MUTATED`
TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-G3-A7M9 TCGA-KR-A7K0 TCGA-T1-A6J8 TCGA-UB-A7MF 
       17.98        26.83         1.84         2.14         0.76         7.04 
TCGA-ZP-A9D1 TCGA-2Y-A9GZ TCGA-2Y-A9H5 TCGA-BC-A10R TCGA-BD-A3EP TCGA-CC-A7II 
        0.69        27.88        18.25        10.13        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-A4NJ TCGA-DD-AACH TCGA-DD-AACZ TCGA-DD-AAE0 TCGA-DD-AAEK 
       30.15        30.51         6.41         5.62        18.25        35.08 
TCGA-ED-A82E TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A5SL TCGA-G3-A5SM 
       13.41         0.20        23.97        27.88        20.42        17.10 
TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-RC-A6M5 TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-WQ-AB4B 
       11.80        27.25         0.49        36.10        19.76        12.99 
TCGA-YA-A8S7 
       13.55 

$`17Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       18.90        23.64         9.96        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K7 
       81.73        30.74        22.13        22.06        20.75        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS 
       12.72        24.56        10.32        29.52        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 
       53.39        63.75        41.79        80.28        24.89       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       40.41        56.91        49.84        47.74        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        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-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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       12.72        18.48        44.81         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-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC 
        0.46        21.76        51.29        90.71        79.40        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65        11.47        12.95        49.15         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL 
       13.78        30.61        33.14        30.97        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
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-AAD0 TCGA-DD-AAD1 
       50.33        46.82         5.59        47.67         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       19.30        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        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        90.48        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        60.99        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-EP-A12J TCGA-EP-A26S 
       14.04        13.15        13.35         1.84        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       19.10        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-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-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-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       16.83        11.80        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M6 
       26.27        17.69        21.01         3.09         0.72         0.30 
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        27.88 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
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 

  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              20.12 
[1] "0.2 - 66.3 (18.0)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.6"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q LOSS MUTATED        10       12         0          9          2
  17Q LOSS WILD-TYPE     163       75         3         53          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q LOSS MUTATED            2        1         1         0
  17Q LOSS WILD-TYPE          5        1         0         2
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  10                163
  STAGE II                 12                 75
  STAGE III                 0                  3
  STAGE IIIA                9                 53
  STAGE IIIB                2                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED    14  13  12   1
  17Q LOSS WILD-TYPE 169  82  65  11
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               14                169
  T2               13                 82
  T3               12                 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"
D72V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    24   2
  17Q LOSS WILD-TYPE 230   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     24    2
  17Q LOSS WILD-TYPE  230    1
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               24                230
  1                2                  1
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    30   1
  17Q LOSS WILD-TYPE 236   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     30    1
  17Q LOSS WILD-TYPE  236    3
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               30                236
  1                1                  3
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    16  24
  17Q LOSS WILD-TYPE 102 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     16   24
  17Q LOSS WILD-TYPE  102  228
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               16                102
  MALE                 24                228
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    36   0
  17Q LOSS WILD-TYPE 302   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     36    0
  17Q LOSS WILD-TYPE  302    9
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                36                302
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17Q LOSS MUTATED                         2                       35
  17Q LOSS WILD-TYPE                       1                      325
                    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                         2                  1
  HEPATOCELLULAR CARCINOMA                       35                325
  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    37   1   0   2
  17Q LOSS WILD-TYPE 287  16   1  19
D72V10, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               37                287
  R1                1                 16
  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                                  1    10
  17Q LOSS WILD-TYPE                                1   148
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           2    26
  17Q LOSS WILD-TYPE                        15   157
D72V11, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          10                148
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          26                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"
D72V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2  33
  17Q LOSS WILD-TYPE  14 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   33
  17Q LOSS WILD-TYPE   14  302
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               33                302
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    46  26
  18P LOSS WILD-TYPE 189 103
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                72                292 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                26                103 
$`18P LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A4NI TCGA-DD-AAEG TCGA-ES-A2HS TCGA-KR-A7K7 TCGA-T1-A6J8 
        5.03        26.83        23.64        22.62        31.27         0.76 
TCGA-ZS-A9CE TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-A10R 
       40.80        49.84        20.81         0.66        14.76        10.13 
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-A4NO TCGA-DD-A73E TCGA-DD-A73G 
        5.62        20.12        32.52        73.81         1.45       114.35 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACI 
        0.53        76.41        55.40        12.53        71.80        53.19 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD5 
       42.81        61.68        13.64        50.33         5.62        44.22 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADO TCGA-DD-AAE2 TCGA-DD-AAEK 
       22.09        40.54        35.67        14.89        20.98        35.08 
TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
       80.71        29.92         0.20        13.15        13.41         1.84 
TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-MI-A75G 
       27.88         0.33        13.68        11.80         2.14        22.95 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7SF TCGA-RC-A7SK 
       10.85        26.27         0.72         0.49        19.04        15.52 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-WX-AA47 TCGA-YA-A8S7 TCGA-ZS-A9CG 
       27.88        19.76        16.44        18.28        13.55        11.21 

$`18P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
       18.90         9.96         8.12         6.38        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG 
       22.13        22.06         1.84        20.75         2.14        12.72 
TCGA-MI-A75H TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-2Y-A9GS 
       24.56         7.04        10.32        29.52         0.69        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H9 
      120.82        40.41        56.91        47.74        18.25        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C 
        1.18         8.55        13.02        10.78        10.59        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-A216 
       27.52         2.99        25.32        23.38         1.12        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-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45         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-A3MC 
        4.24         3.35         3.32         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-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS 
       13.12        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-A119 
        8.15        79.73        37.78        83.57        53.33         7.33 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65        11.47        45.11        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       17.59       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 
        9.30        23.05        22.78        35.67        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       75.65        12.00        15.42         6.41        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
        3.52        58.16        14.20        59.31        51.35        51.52 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       42.58        40.08        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
        3.78        37.64        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       29.52        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 
       19.30        18.25        18.25        18.15        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        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        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       60.99        53.69        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K 
        9.73        12.82         0.20        14.04        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        60.89        23.97        19.10        12.03         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        51.06        53.79        28.27        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14        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 
       11.64        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        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-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M6 TCGA-RC-A7S9 
       58.88        17.69        21.01         3.09         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       19.33        15.39        36.10         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-XR-A8TD 
       11.34         0.99        12.99        20.22        24.85        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       30.41        22.78        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       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              19.99 
[1] "0.2 - 114.3 (18.7)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED        33       20         0         13          0
  18P LOSS WILD-TYPE     140       67         3         49          9
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P LOSS MUTATED            2        1         1         0
  18P LOSS WILD-TYPE          5        1         0         2
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  33                140
  STAGE II                 20                 67
  STAGE III                 0                  3
  STAGE IIIA               13                 49
  STAGE IIIB                0                  9
  STAGE IIIC                2                  5
  STAGE IV                  1                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED    37  21  15   1
  18P LOSS WILD-TYPE 146  74  62  11
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               37                146
  T2               21                 74
  T3               15                 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"
D73V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    52   2
  18P LOSS WILD-TYPE 202   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     52    2
  18P LOSS WILD-TYPE  202    1
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               52                202
  1                2                  1
[1] 2 2
[1] FALSE
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    58   1
  18P LOSS WILD-TYPE 208   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     58    1
  18P LOSS WILD-TYPE  208    3
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               58                208
  1                1                  3
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    29  45
  18P LOSS WILD-TYPE  89 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     29   45
  18P LOSS WILD-TYPE   89  207
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               29                 89
  MALE                 45                207
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    63   3
  18P LOSS WILD-TYPE 275   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     63    3
  18P LOSS WILD-TYPE  275    6
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                63                275
  YES                3                  6
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18P LOSS MUTATED                         3                       68
  18P LOSS WILD-TYPE                       0                      292
                    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                         3                  0
  HEPATOCELLULAR CARCINOMA                       68                292
  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    66   3   0   5
  18P LOSS WILD-TYPE 258  14   1  16
D73V10, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               66                258
  R1                3                 14
  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                                2   124
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           2    38
  18P LOSS WILD-TYPE                        15   145
D73V11, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          34                124
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          38                145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  67
  18P LOSS WILD-TYPE  13 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   67
  18P LOSS WILD-TYPE   13  268
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               67                268
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    52  25
  18Q LOSS WILD-TYPE 183 104
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                77                287 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                25                104 
$`18Q LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A4NI TCGA-DD-AAEG TCGA-ES-A2HS TCGA-KR-A7K7 TCGA-T1-A6J8 
        5.03        26.83        23.64        22.62        31.27         0.76 
TCGA-UB-A7MF TCGA-ZS-A9CE TCGA-2Y-A9H3 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D 
        7.04        40.80        49.84        10.59         0.66        14.76 
TCGA-BC-A10R TCGA-BC-A216 TCGA-BC-A217 TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A7IK 
       10.13        44.42        45.93        10.36         9.99         8.61 
TCGA-CC-A8HV TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EJ 
        9.17       113.00         2.60         0.46        12.95        33.04 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NO 
       13.64        55.69         5.62        30.61        32.52        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        71.80 
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-AAEK TCGA-DD-AAVP TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A66X 
       20.98        35.08        90.48        80.71        29.92        13.35 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S 
       13.15        13.41         1.84        27.88         0.33        13.68 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-MI-A75G TCGA-MR-A8JO 
       14.70        11.80         2.14        28.90        22.95        10.85 
TCGA-NI-A8LF TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 
       26.27         0.72         0.49        19.04        15.52        36.10 
TCGA-UB-A7MC TCGA-WX-AA44 TCGA-WX-AA47 TCGA-YA-A8S7 TCGA-ZS-A9CG 
       16.44        20.22        18.28        13.55        11.21 

$`18Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
       18.90         9.96         8.12         6.38        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG 
       22.13        22.06         1.84        20.75         2.14        12.72 
TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-2Y-A9GS TCGA-2Y-A9GT 
       24.56        10.32        29.52         0.69        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       63.75        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       40.41        56.91        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5R-AA1C TCGA-5R-AAAM 
        1.18         8.55        13.02        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-A3KF TCGA-BC-A3KG 
        2.99        25.32        23.38         1.12         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       14.60        12.72        18.48        44.81        13.45         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-A3MC TCGA-CC-A5UC TCGA-CC-A5UE 
        3.32         9.86         9.96        11.93        11.41         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        7.13        21.34         9.83        12.00        13.12        12.56 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        9.14         4.60        11.31         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D 
       37.78        83.57        53.33         7.33        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       45.11        49.15         6.02        18.35        21.14        27.19 
TCGA-DD-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-A4NF TCGA-DD-A4NH 
      102.74       107.11        13.78        33.14        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-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        23.93        23.05        22.78 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
       35.67        13.48        11.41        75.65        55.40        12.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW 
       58.16        14.20        59.31        51.35        51.52        46.82 
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-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-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-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY 
       15.06        14.33        66.67        15.58        18.21        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.25        18.15        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVQ 
       15.72        25.08        26.63        25.78        50.33        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-A4XI 
       62.47        66.25        65.39        60.99        53.69        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       28.08        13.91         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       14.04        13.35         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
       19.10        12.03         0.03         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
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-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       13.55         0.89        11.64        11.87         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       29.79        13.97        12.03         9.57        16.67        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M6 
        7.53        58.88        17.69        21.01         3.09         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD 
       21.04        19.33        15.39        27.88        19.76         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       15.98        10.75        11.34         0.99        12.99        24.85 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       33.86        30.41        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       35.87        25.15        12.99        45.57        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 
             16.44              20.12 
[1] "0.3 - 114.3 (16.4)" "0.0 - 120.8 (20.1)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED        37       19         0         15          0
  18Q LOSS WILD-TYPE     136       68         3         47          9
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q LOSS MUTATED            2        1         1         1
  18Q LOSS WILD-TYPE          5        1         0         1
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  37                136
  STAGE II                 19                 68
  STAGE III                 0                  3
  STAGE IIIA               15                 47
  STAGE IIIB                0                  9
  STAGE IIIC                2                  5
  STAGE IV                  1                  1
  STAGE IVA                 1                  0
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q LOSS MUTATED    40  20  17   2
  18Q LOSS WILD-TYPE 143  75  60  10
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               40                143
  T2               20                 75
  T3               17                 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"
D74V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    55   2
  18Q LOSS WILD-TYPE 199   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     55    2
  18Q LOSS WILD-TYPE  199    1
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               55                199
  1                2                  1
[1] 2 2
[1] FALSE
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    60   2
  18Q LOSS WILD-TYPE 206   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     60    2
  18Q LOSS WILD-TYPE  206    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               60                206
  1                2                  2
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    30  49
  18Q LOSS WILD-TYPE  88 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     30   49
  18Q LOSS WILD-TYPE   88  203
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               30                 88
  MALE                 49                203
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    66   4
  18Q LOSS WILD-TYPE 272   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     66    4
  18Q LOSS WILD-TYPE  272    5
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                66                272
  YES                4                  5
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18Q LOSS MUTATED                         3                       74
  18Q LOSS WILD-TYPE                       0                      286
                    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                         3                  0
  HEPATOCELLULAR CARCINOMA                       74                286
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED    70   2   0   7
  18Q LOSS WILD-TYPE 254  15   1  14
D74V10, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               70                254
  R1                2                 15
  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                                2   123
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           3    41
  18Q LOSS WILD-TYPE                        14   142
D74V11, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          35                123
  BLACK OR AFRICAN AMERICAN                       3                 14
  WHITE                                          41                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"
D74V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     5  69
  18Q LOSS WILD-TYPE  11 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5   69
  18Q LOSS WILD-TYPE   11  266
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 11
  NOT HISPANIC OR LATINO               69                266
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    26  24
  19P LOSS WILD-TYPE 209 105
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                50                314 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                24                105 
$`19P LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-AADV TCGA-DD-AAE8 TCGA-T1-A6J8 TCGA-2Y-A9GS TCGA-2Y-A9GY 
        5.03        18.87        21.83         0.76        23.80        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-BC-A10W TCGA-BC-A3KF 
       27.88       120.82        56.91        49.84         2.99         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-A1EG TCGA-DD-A1EI 
        9.83         8.61         9.14         2.60        45.11         6.02 
TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NJ TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACO 
       33.04         5.62        30.51        71.80        15.42        61.68 
TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AADC 
       13.64        59.31        51.52        50.33         5.62        13.97 
TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AAVR TCGA-DD-AAVV TCGA-ED-A8O6 TCGA-ED-A97K 
       40.47        20.91        82.62        80.71         1.84         0.20 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A3CH TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-RC-A6M4 
        0.33        13.68        25.64        20.78        11.80         0.72 
TCGA-RG-A7D4 TCGA-ZP-A9CV 
       36.10        35.77 

$`19P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAEA 
       36.66         0.36        90.28        26.83        21.17        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       23.64         9.96        22.62         8.12         6.38        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       30.74        22.13        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       31.27        12.72        24.56         7.04        10.32        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
        0.69        40.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       40.41        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55        13.02        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-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52        27.52        25.32        23.38         1.12 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       44.42        45.93        22.36        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       44.81        13.45         0.66         2.86         3.19         3.39 
TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.35         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HU 
        7.13        12.00        13.12        12.56         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-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       12.95        49.15        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       32.52        30.97        30.15        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       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-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-AACN TCGA-DD-AACQ TCGA-DD-AACT 
        0.30         3.52        58.16        42.81        14.20        51.35 
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-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-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        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        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       89.69        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        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-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-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-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.03         0.39        51.06        53.79        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
       22.95        20.42        17.10        14.70        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        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        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-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        3.09         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
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-A9CF TCGA-ZS-A9CG 
       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 
            17.145             19.890 
[1] "0.2 - 120.8 (17.1)" "0.0 - 114.3 (19.9)"
[1] "hr=" "1.6"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED        23        9         0         12          1
  19P LOSS WILD-TYPE     150       78         3         50          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P LOSS MUTATED            2        0         0         0
  19P LOSS WILD-TYPE          5        2         1         2
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  23                150
  STAGE II                  9                 78
  STAGE III                 0                  3
  STAGE IIIA               12                 50
  STAGE IIIB                1                  8
  STAGE IIIC                2                  5
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED    26  10  13   3
  19P LOSS WILD-TYPE 157  85  64   9
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               26                157
  T2               10                 85
  T3               13                 64
  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    37   1
  19P LOSS WILD-TYPE 217   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     37    1
  19P LOSS WILD-TYPE  217    2
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               37                217
  1                1                  2
[1] 2 2
[1] FALSE
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    41   0
  19P LOSS WILD-TYPE 225   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     41    0
  19P LOSS WILD-TYPE  225    4
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               41                225
  1                0                  4
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    12  40
  19P LOSS WILD-TYPE 106 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     12   40
  19P LOSS WILD-TYPE  106  212
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               12                106
  MALE                 40                212
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    44   0
  19P LOSS WILD-TYPE 294   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     44    0
  19P LOSS WILD-TYPE  294    9
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                44                294
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19P LOSS MUTATED                         0                       51
  19P LOSS WILD-TYPE                       3                      309
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19P LOSS MUTATED                                  1
  19P LOSS WILD-TYPE                                6
D75V9, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  3
  HEPATOCELLULAR CARCINOMA                       51                309
  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
  19P LOSS MUTATED    44   3   0   4
  19P LOSS WILD-TYPE 280  14   1  17
D75V10, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               44                280
  R1                3                 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
  19P LOSS MUTATED                                  0    32
  19P LOSS WILD-TYPE                                2   126
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           2    18
  19P LOSS WILD-TYPE                        15   165
D75V11, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          32                126
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          18                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"
D75V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3  48
  19P LOSS WILD-TYPE  13 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3   48
  19P LOSS WILD-TYPE   13  287
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               48                287
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    20  17
  19Q LOSS WILD-TYPE 215 112
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                37                327 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                17                112 
$`19Q LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-AADV TCGA-DD-AAE8 TCGA-T1-A6J8 TCGA-2Y-A9GS TCGA-2Y-A9GY 
        5.03        18.87        21.83         0.76        23.80        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT 
       27.88       120.82         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-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NJ TCGA-DD-AACE 
        2.60         6.02        33.04         5.62        30.51        71.80 
TCGA-DD-AACO TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AADD TCGA-DD-AADL 
       61.68        59.31        51.52        50.33        40.47        20.91 
TCGA-DD-AAVR TCGA-DD-AAVW TCGA-ED-A8O6 TCGA-G3-AAV1 TCGA-RC-A6M4 TCGA-RC-A7SK 
       82.62        76.18         1.84        11.80         0.72        15.52 
TCGA-RG-A7D4 
       36.10 

$`19Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAEA 
       36.66         0.36        90.28        26.83        21.17        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       23.64         9.96        22.62         8.12         6.38        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       30.74        22.13        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       31.27        12.72        24.56         7.04        10.32        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
        0.69        40.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       40.41        56.91        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        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-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       25.32        23.38         1.12        44.42        45.93        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       14.60        12.72        18.48        44.81        13.45         0.66 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.19         3.39         3.35         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7II 
       10.36        11.93        11.41         7.13        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
       12.56         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-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       18.35        13.64        21.14        27.19        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78        30.61        33.14        32.52        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-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-AACP TCGA-DD-AACQ TCGA-DD-AACT 
        3.52        58.16        42.81        13.64        14.20        51.35 
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-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.83        13.97        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       35.08        90.48        89.69        59.93        72.39        80.71 
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        60.99 
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-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41        13.35         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14        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 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
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-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
       21.01         3.09         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       19.04        15.39        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        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 

  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 
             18.87              19.79 
[1] "0.3 - 120.8 (18.9)" "0.0 - 114.3 (19.8)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED        17        6         0         10          1
  19Q LOSS WILD-TYPE     156       81         3         52          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q LOSS MUTATED            2        0         0         0
  19Q LOSS WILD-TYPE          5        2         1         2
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  17                156
  STAGE II                  6                 81
  STAGE III                 0                  3
  STAGE IIIA               10                 52
  STAGE IIIB                1                  8
  STAGE IIIC                2                  5
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED    19   7  11   2
  19Q LOSS WILD-TYPE 164  88  66  10
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               19                164
  T2                7                 88
  T3               11                 66
  T4                2                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    29   1
  19Q LOSS WILD-TYPE 225   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     29    1
  19Q LOSS WILD-TYPE  225    2
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               29                225
  1                1                  2
[1] 2 2
[1] FALSE
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    33   0
  19Q LOSS WILD-TYPE 233   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     33    0
  19Q LOSS WILD-TYPE  233    4
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               33                233
  1                0                  4
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     8  31
  19Q LOSS WILD-TYPE 110 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8   31
  19Q LOSS WILD-TYPE  110  221
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                8                110
  MALE                 31                221
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    32   0
  19Q LOSS WILD-TYPE 306   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     32    0
  19Q LOSS WILD-TYPE  306    9
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                32                306
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19Q LOSS MUTATED                         0                       39
  19Q LOSS WILD-TYPE                       3                      321
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19Q LOSS MUTATED                                  0
  19Q LOSS WILD-TYPE                                7
D76V9, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  3
  HEPATOCELLULAR CARCINOMA                       39                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
  19Q LOSS MUTATED    33   1   0   4
  19Q LOSS WILD-TYPE 291  16   1  17
D76V10, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               33                291
  R1                1                 16
  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    26
  19Q LOSS WILD-TYPE                                2   132
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           2    11
  19Q LOSS WILD-TYPE                        15   172
D76V11, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          26                132
  BLACK OR AFRICAN AMERICAN                       2                 15
  WHITE                                          11                172
[1] 4 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  36
  19Q LOSS WILD-TYPE  14 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   36
  19Q LOSS WILD-TYPE   14  299
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               36                299
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    17   8
  20P LOSS WILD-TYPE 218 121
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                25                339 
  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 
TCGA-XR-A8TD 
       33.86 

$`20P LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        38.40         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD 
       20.81        22.92         1.18         8.55        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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
       44.42        45.93         0.26        22.36        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       18.48        44.81        13.45         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-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
        9.96        10.36        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT 
       21.34         9.83        12.00        13.12         8.61         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
       11.31         9.17         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-A1EL 
       12.95        45.11        49.15         6.02        33.04        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        27.19        55.69        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       70.06        20.12       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-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        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        51.35        51.52        50.33        46.82 
TCGA-DD-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-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-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-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-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        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        60.99        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-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-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
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-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        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        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       20.22        24.85        18.28        30.41        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 

  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 
             12.56              20.42 
[1] "0.2 - 102.7 (12.6)" "0.0 - 120.8 (20.4)"
[1] "hr=" "1"  
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P LOSS MUTATED         9        8         1          5          2
  20P LOSS WILD-TYPE     164       79         2         57          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P LOSS MUTATED            0        0         0         1
  20P LOSS WILD-TYPE          7        2         1         1
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   9                164
  STAGE II                  8                 79
  STAGE III                 1                  2
  STAGE IIIA                5                 57
  STAGE IIIB                2                  7
  STAGE IIIC                0                  7
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED     9   8   8   1
  20P LOSS WILD-TYPE 174  87  69  11
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                9                174
  T2                8                 87
  T3                8                 69
  T4                1                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    23   0
  20P LOSS WILD-TYPE 231   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     23    0
  20P LOSS WILD-TYPE  231    3
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               23                231
  1                0                  3
[1] 2 2
[1] FALSE
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    21   1
  20P LOSS WILD-TYPE 245   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     21    1
  20P LOSS WILD-TYPE  245    3
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               21                245
  1                1                  3
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     9  17
  20P LOSS WILD-TYPE 109 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      9   17
  20P LOSS WILD-TYPE  109  235
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                9                109
  MALE                 17                235
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    23   1
  20P LOSS WILD-TYPE 315   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     23    1
  20P LOSS WILD-TYPE  315    8
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                23                315
  YES                1                  8
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20P LOSS MUTATED                         1                       24
  20P LOSS WILD-TYPE                       2                      336
                    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                  2
  HEPATOCELLULAR CARCINOMA                       24                336
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    24   0   0   2
  20P LOSS WILD-TYPE 300  17   1  19
D77V10, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               24                300
  R1                0                 17
  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                                  1    13
  20P LOSS WILD-TYPE                                1   145
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           1    11
  20P LOSS WILD-TYPE                        16   172
D77V11, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          13                145
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                          11                172
[1] 4 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     2  22
  20P LOSS WILD-TYPE  14 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   22
  20P LOSS WILD-TYPE   14  313
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               22                313
[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 226 126
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                12                352 
  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-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        38.40         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH 
       20.81        22.92         1.18         8.55        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        17.10         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-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       14.60        12.72        18.48        44.81        13.45         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-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-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-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-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-A3A9 
       70.06        17.59        20.12       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-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-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        71.80        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-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-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-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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        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        90.48        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        60.99        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-A8O6 
       12.82         0.20        14.04        13.15        13.41         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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
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-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        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        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       12.99        45.57        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             19.990 
[1] "5.6 - 102.7 (13.2)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.7"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q LOSS MUTATED         5        4         1          2          1
  20Q LOSS WILD-TYPE     168       83         2         60          8
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q LOSS MUTATED            0        0         0         0
  20Q LOSS WILD-TYPE          7        2         1         2
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   5                168
  STAGE II                  4                 83
  STAGE III                 1                  2
  STAGE IIIA                2                 60
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     5   4   4   0
  20Q LOSS WILD-TYPE 178  91  73  12
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                5                178
  T2                4                 91
  T3                4                 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"
D78V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    10   0
  20Q LOSS WILD-TYPE 244   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     10    0
  20Q LOSS WILD-TYPE  244    3
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0               10                244
  1                0                  3
[1] 2 2
[1] FALSE
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    10   0
  20Q LOSS WILD-TYPE 256   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     10    0
  20Q LOSS WILD-TYPE  256    4
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0               10                256
  1                0                  4
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   8
  20Q LOSS WILD-TYPE 113 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    8
  20Q LOSS WILD-TYPE  113  244
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                5                113
  MALE                  8                244
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    11   1
  20Q LOSS WILD-TYPE 327   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     11    1
  20Q LOSS WILD-TYPE  327    8
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                11                327
  YES                1                  8
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20Q LOSS MUTATED                         1                       12
  20Q LOSS WILD-TYPE                       2                      348
                    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                  2
  HEPATOCELLULAR CARCINOMA                       12                348
  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    11   0   0   2
  20Q LOSS WILD-TYPE 313  17   1  19
D78V10, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               11                313
  R1                0                 17
  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                                  1     4
  20Q LOSS WILD-TYPE                                1   154
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           1     7
  20Q LOSS WILD-TYPE                        16   176
D78V11, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           4                154
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           7                176
[1] 4 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  15 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   10
  20Q LOSS WILD-TYPE   15  325
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               10                325
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    63  44
  21Q LOSS WILD-TYPE 172  85
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               107                257 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                44                 85 
$`21Q LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A4NI TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A4ZP 
        5.03        26.83        21.83        23.64         9.96        81.73 
TCGA-G3-A7M9 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-UB-A7MF 
        1.84         2.14        31.27        12.72         0.76         7.04 
TCGA-ZP-A9D1 TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9HB 
        0.69        80.28        24.89        49.84        18.25         8.55 
TCGA-5C-A9VH TCGA-5R-AA1C TCGA-BC-A10U TCGA-BC-A216 TCGA-BC-A69H TCGA-BD-A3EP 
       10.59        17.10        27.52        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-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACE 
       32.52       114.35        13.48         0.53        12.53        71.80 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACU 
       15.42        53.19         0.30        42.81        13.64        51.52 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC 
       47.67         5.62        21.63        22.09        40.08        13.97 
TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       40.47        20.91        29.52        15.06        14.33        66.67 
TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAW2 
       18.25        18.61        26.63        59.93        80.71        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-EP-A2KC 
       53.69        29.92         9.73         0.20         0.20         0.62 
TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Z 
       11.93        60.89        23.97         0.33        13.68        21.53 
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-MI-A75E TCGA-MR-A8JO TCGA-RC-A6M6 TCGA-RC-A7SF 
       17.06        11.80        16.67        10.85         0.30        19.04 
TCGA-RG-A7D4 TCGA-WQ-AB4B TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       36.10        12.99        22.78        13.55        35.77 

$`21Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAEA 
       36.66         0.36        90.28        18.87        21.17        18.90 
TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
       22.62         8.12         6.38        30.74        22.13        22.06 
TCGA-K7-A5RF TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS 
       20.75        24.56        10.32        29.52        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       53.39        63.75        41.79        27.88       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 
       56.91        47.74        20.81        22.92         1.18        13.02 
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
       10.78         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-A10Z TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I 
       23.38         1.12        45.93         0.26        22.36        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       18.48        44.81         0.66         4.24         2.86         3.19 
TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE 
        4.24         9.86         9.96        11.93        11.41         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A8HT 
        7.13        21.34         9.83        12.00         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
       11.31         6.94        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
      113.00         0.46        21.76        51.29        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39W 
       19.79        75.65        11.47         6.02        18.35        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       55.69        19.76        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
      107.11        33.14        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
        1.45        35.67        11.41        75.65        76.41        55.40 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO 
       12.00         6.41        69.11         3.52        58.16        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.35        50.33        46.82         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADB 
        4.50        18.54        42.58        44.22        40.54        40.83 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 
        0.39        14.89        15.58        18.21        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15        20.98        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       82.62        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       66.25        65.39        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-ES-A2HT 
        0.20        18.74        19.99        20.61        19.59        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
       19.10        27.88        12.03         0.03         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        58.49        14.86        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-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-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       11.64        11.87        28.90         1.02         2.20         2.99 
TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       16.83        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       22.95        20.71         7.53        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SB 
       21.01         3.09         0.72         0.49        21.04        19.33 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        10.75        11.34         0.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       18.28        33.86        30.41        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        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 
             14.60              20.78 
[1] "0.2 - 114.3 (14.6)" "0.0 - 120.8 (20.8)"
[1] "hr=" "1.5"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED        52       25         1         17          2
  21Q LOSS WILD-TYPE     121       62         2         45          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q LOSS MUTATED            4        2         0         1
  21Q LOSS WILD-TYPE          3        0         1         1
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  52                121
  STAGE II                 25                 62
  STAGE III                 1                  2
  STAGE IIIA               17                 45
  STAGE IIIB                2                  7
  STAGE IIIC                4                  3
  STAGE IV                  2                  0
  STAGE IVA                 0                  1
  STAGE IVB                 1                  1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q LOSS MUTATED    56  27  22   4
  21Q LOSS WILD-TYPE 127  68  55   8
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               56                127
  T2               27                 68
  T3               22                 55
  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    76   1
  21Q LOSS WILD-TYPE 178   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     76    1
  21Q LOSS WILD-TYPE  178    2
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               76                178
  1                1                  2
[1] 2 2
[1] FALSE
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    84   3
  21Q LOSS WILD-TYPE 182   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     84    3
  21Q LOSS WILD-TYPE  182    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               84                182
  1                3                  1
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    27  83
  21Q LOSS WILD-TYPE  91 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     27   83
  21Q LOSS WILD-TYPE   91  169
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               27                 91
  MALE                 83                169
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   100   2
  21Q LOSS WILD-TYPE 238   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    100    2
  21Q LOSS WILD-TYPE  238    7
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO               100                238
  YES                2                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  21Q LOSS MUTATED                         2                      106
  21Q LOSS WILD-TYPE                       1                      254
                    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                  1
  HEPATOCELLULAR CARCINOMA                      106                254
  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    95   5   1   5
  21Q LOSS WILD-TYPE 229  12   0  16
D79V10, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               95                229
  R1                5                 12
  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    51
  21Q LOSS WILD-TYPE                                2   107
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           6    49
  21Q LOSS WILD-TYPE                        11   134
D79V11, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                          51                107
  BLACK OR AFRICAN AMERICAN                       6                 11
  WHITE                                          49                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"
D79V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     5  98
  21Q LOSS WILD-TYPE  11 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5   98
  21Q LOSS WILD-TYPE   11  237
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 11
  NOT HISPANIC OR LATINO               98                237
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    41  26
  22Q LOSS WILD-TYPE 194 103
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                67                297 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                26                103 
$`22Q LOSS MUTATED`
TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-T1-A6J8 
       17.98        26.83        81.73         1.84        31.27         0.76 
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-A8YO TCGA-BD-A3EP 
       37.32        27.52        45.93         0.26        18.48        13.45 
TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A5UD TCGA-CC-A7IK TCGA-CC-A8HU 
        2.86         3.35         3.32         9.99         8.61        11.31 
TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A39X TCGA-DD-A39Y 
        9.17        79.73        37.78         2.60        55.69         5.62 
TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73B 
      107.11        32.52        30.51        73.81       108.76         9.30 
TCGA-DD-AAC8 TCGA-DD-AACZ TCGA-DD-AADF TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AAE3 
        0.53         5.62         3.78        14.33        15.58        18.61 
TCGA-DD-AAEE TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP 
       26.63        29.92         9.73         0.20        14.04        13.15 
TCGA-EP-A2KB TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SI TCGA-G3-A7M5 TCGA-G3-AAV3 
       19.59        13.68        51.06        25.25        14.70        13.55 
TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO 
       17.06        11.80        27.25        22.95        20.71        10.85 
TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WQ-AB4B 
        3.09         0.49         0.30        36.10        16.44        12.99 
TCGA-XR-A8TD 
       33.86 

$`22Q LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       18.90        23.64         9.96        22.62         8.12         6.38 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG 
       30.74        22.13        22.06        20.75         2.14        12.72 
TCGA-MI-A75H TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       24.56         7.04        10.32        29.52         0.69        40.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       40.41        56.91        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM 
        8.55        13.02        10.59         0.66        17.10         1.51 
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69H 
       25.32        23.38         1.12        44.42        22.36        14.60 
TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       12.72        44.81         0.66         4.24         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        4.24         9.86         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-A7IL TCGA-CC-A8HT TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A115 
       12.56         9.14         4.60         6.94         8.15        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-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-A3A7 TCGA-DD-A3A9 
       70.06        17.59        20.12       102.74        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       33.14        30.97        30.15        39.78        56.25        29.56 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       12.26         0.30        80.75        78.84        23.93        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 
       22.78         1.45        35.67       114.35        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-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-AADR TCGA-DD-AADU TCGA-DD-AADW 
       29.52        14.89        15.06        66.67        18.21        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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       23.74        15.72        25.08        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        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 
       60.99        53.69        26.93        28.08        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       12.82         0.20        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.33         0.39        53.79        28.27        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       21.53        25.64         5.92        19.53        19.23        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       20.42        17.10        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       15.65        11.80        12.23         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       16.83        29.79        13.97        12.03         9.57        16.67 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A6M4 
        7.53        58.88        26.27        17.69        21.01         0.72 
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        27.88 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       19.76         1.71        15.98        10.75        11.34         0.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       20.22        24.85        18.28        30.41        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 

  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 
             15.58              20.61 
[1] "0.2 - 120.8 (15.6)" "0.0 - 114.3 (20.6)"
[1] "hr=" "1.2"
D80V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED        23       23         0         13          2
  22Q LOSS WILD-TYPE     150       64         3         49          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q LOSS MUTATED            2        1         1         0
  22Q LOSS WILD-TYPE          5        1         0         2
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  23                150
  STAGE II                 23                 64
  STAGE III                 0                  3
  STAGE IIIA               13                 49
  STAGE IIIB                2                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  1
  STAGE IVA                 1                  0
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED    25  27  15   3
  22Q LOSS WILD-TYPE 158  68  62   9
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               25                158
  T2               27                 68
  T3               15                 62
  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    45   1
  22Q LOSS WILD-TYPE 209   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     45    1
  22Q LOSS WILD-TYPE  209    2
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               45                209
  1                1                  2
[1] 2 2
[1] FALSE
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    54   1
  22Q LOSS WILD-TYPE 212   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     54    1
  22Q LOSS WILD-TYPE  212    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               54                212
  1                1                  3
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    26  44
  22Q LOSS WILD-TYPE  92 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     26   44
  22Q LOSS WILD-TYPE   92  208
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               26                 92
  MALE                 44                208
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    61   2
  22Q LOSS WILD-TYPE 277   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     61    2
  22Q LOSS WILD-TYPE  277    7
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                61                277
  YES                2                  7
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  22Q LOSS MUTATED                         3                       65
  22Q LOSS WILD-TYPE                       0                      295
                    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                         3                  0
  HEPATOCELLULAR CARCINOMA                       65                295
  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    55   6   0   8
  22Q LOSS WILD-TYPE 269  11   1  13
D80V10, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               55                269
  R1                6                 11
  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                                  1    22
  22Q LOSS WILD-TYPE                                1   136
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           8    39
  22Q LOSS WILD-TYPE                         9   144
D80V11, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                          22                136
  BLACK OR AFRICAN AMERICAN                       8                  9
  WHITE                                          39                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"
D80V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     6  57
  22Q LOSS WILD-TYPE  10 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   57
  22Q LOSS WILD-TYPE   10  278
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 10
  NOT HISPANIC OR LATINO               57                278
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    65  28
  XP LOSS WILD-TYPE 170 101
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               93               271 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               28               101 
$`XP LOSS MUTATED`
TCGA-2Y-A9H6 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-AADV TCGA-DD-AAE8 TCGA-ES-A2HS 
       11.74         5.03        17.98        18.87        21.83        22.62 
TCGA-G3-A6UC TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-ZS-A9CE TCGA-2Y-A9GS 
       22.06        31.27         0.76         7.04        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-5C-AAPD 
       53.39        63.75        41.79        56.91        47.74         0.66 
TCGA-5R-AA1C TCGA-BC-A217 TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A3MA TCGA-CC-A5UD 
       17.10        45.93         0.66         3.35         9.96         9.99 
TCGA-CC-A5UE TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A9FS TCGA-DD-A114 
        8.94         9.83        12.00         9.14         6.94        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A39V TCGA-DD-A4NA 
       83.57        53.33         2.60         0.46        21.14        33.14 
TCGA-DD-A4NF TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-AACG TCGA-DD-AACI 
       30.97        73.81        78.84         9.30        15.42        53.19 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       42.81        61.68        59.31        51.52        50.33        46.82 
TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADL TCGA-DD-AADP 
       47.67        44.22        40.08        13.97        20.91        15.06 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVP 
       19.30        18.25        20.98        25.08        25.78        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ 
       89.69        72.39        65.39        29.92         0.20         0.20 
TCGA-ED-A97K TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U 
        0.20        19.10        27.88         0.33        13.68        53.79 
TCGA-G3-A7M5 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
       14.70        15.65        12.23        13.55         0.89        11.87 
TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-LG-A9QC TCGA-MI-A75E TCGA-MI-A75G TCGA-QA-A7B7 
       37.71        16.83        13.97        16.67        22.95         3.09 
TCGA-RC-A6M4 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MC TCGA-ZP-A9CV 
        0.72        19.33        15.39        15.52        16.44        35.77 
TCGA-ZP-A9D2 TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        79.30        11.21 

$`XP LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A3A8 
       83.24        38.40         8.61        69.57        36.66         0.36 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL 
       90.28        26.83        21.17        18.90        23.64         9.96 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A7M9 
        8.12         6.38        81.73        30.74        22.13         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG 
       20.75         2.14        12.72        24.56        10.32        29.52 
TCGA-ZP-A9D1 TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
        0.69        80.28        24.89        27.88       120.82        40.41 
TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       49.84        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       13.02        10.78        10.59        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-A216 TCGA-BC-A3KF 
        2.99        25.32        23.38         1.12        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        14.60        12.72        18.48        44.81        13.45 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        4.24         2.86         3.19         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IF 
        9.86        10.36        11.93        11.41         7.13        21.34 
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-A11C TCGA-DD-A11D 
        8.15        79.73       113.00         7.33        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        27.19        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       13.78        30.61        32.52        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56       108.76        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       23.93        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       12.53        71.80        12.00         6.41        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACX 
        3.52        58.16        13.64        14.20        51.35         5.59 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 
        5.62         4.50        18.54        21.63        42.58        22.09 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.54        40.83        40.47        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-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 
       14.33        66.67        15.58        18.21        18.25        18.15 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE 
       18.61        19.99         4.64        23.74        15.72        26.63 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       50.33        35.08        82.62        59.93        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        64.77        62.47        66.25        60.99        53.69 
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-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J 
       14.04        13.15        13.41        13.35         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
       60.89        23.97        12.03         0.03         0.39        51.06 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV5 
       20.78        11.87        14.14        15.78        11.80        11.64 
TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RG 
        2.14        28.90         1.02         2.20         2.99        17.06 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75I 
       11.80        27.25        29.79        12.03         9.57        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-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA 
        0.49         0.30        21.04        19.04        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       19.76         1.71        15.98        10.75        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D4 
       22.78        13.55        25.71        23.21        35.87        12.99 
TCGA-ZS-A9CD 
       45.57 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.20              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            90.48            120.82 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            19.33             19.79 
[1] "0.2 - 90.5 (19.3)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D81V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XP LOSS MUTATED        44       25         0         15          2          2
  XP LOSS WILD-TYPE     129       62         3         47          7          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XP LOSS MUTATED          1         0         0
  XP LOSS WILD-TYPE        1         1         2
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 44               129
  STAGE II                25                62
  STAGE III                0                 3
  STAGE IIIA              15                47
  STAGE IIIB               2                 7
  STAGE IIIC               2                 5
  STAGE IV                 1                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP LOSS MUTATED    46  29  17   2
  XP LOSS WILD-TYPE 137  66  60  10
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              46               137
  T2              29                66
  T3              17                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"
D81V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    66   1
  XP LOSS WILD-TYPE 188   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     66    1
  XP LOSS WILD-TYPE  188    2
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              66               188
  1               1                 2
[1] 2 2
[1] FALSE
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    72   1
  XP LOSS WILD-TYPE 194   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     72    1
  XP LOSS WILD-TYPE  194    3
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              72               194
  1               1                 3
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    19  76
  XP LOSS WILD-TYPE  99 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     19   76
  XP LOSS WILD-TYPE   99  176
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              19                99
  MALE                76               176
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    87   3
  XP LOSS WILD-TYPE 251   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     87    3
  XP LOSS WILD-TYPE  251    6
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               87               251
  YES               3                 6
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XP LOSS MUTATED                         0                       92
  XP LOSS WILD-TYPE                       3                      268
                   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                 3
  HEPATOCELLULAR CARCINOMA                      92               268
  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    84   3   0   8
  XP LOSS WILD-TYPE 240  14   1  13
D81V10, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              84               240
  R1               3                14
  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    47
  XP LOSS WILD-TYPE                                2   111
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                           5    42
  XP LOSS WILD-TYPE                        12   141
D81V11, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         47               111
  BLACK OR AFRICAN AMERICAN                      5                12
  WHITE                                         42               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"
D81V12, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     3  88
  XP LOSS WILD-TYPE  13 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3   88
  XP LOSS WILD-TYPE   13  247
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              88               247
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    49  24
  XQ LOSS WILD-TYPE 186 105
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               73               291 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               24               105 
$`XQ LOSS MUTATED`
TCGA-2Y-A9H6 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-AADV TCGA-DD-AAE8 TCGA-G3-A6UC 
       11.74         5.03        17.98        18.87        21.83        22.06 
TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GU 
       31.27         0.76         7.04        40.80        23.80        63.75 
TCGA-2Y-A9GW TCGA-2Y-A9H2 TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A217 TCGA-CC-A3MA 
       41.79        56.91         0.66        10.13        45.93         9.96 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IG TCGA-CC-A7IL TCGA-CC-A9FS TCGA-DD-A114 
        9.99         8.94         9.83         9.14         6.94        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-A73B 
       83.57        53.33         0.46        33.14        73.81         9.30 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACS TCGA-DD-AACU 
       15.42        53.19        42.81        61.68        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC 
       50.33        46.82        47.67        44.22        40.08        13.97 
TCGA-DD-AADL TCGA-DD-AADP TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAED 
       20.91        15.06        19.30        18.25        20.98        25.08 
TCGA-DD-AAEH TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A97K 
       25.78        72.39        29.92         0.20         0.20         0.20 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-G3-A7M5 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 
       19.10        27.88        14.70        15.65        12.23         0.89 
TCGA-G3-AAV7 TCGA-HP-A5N0 TCGA-LG-A9QC TCGA-MI-A75E TCGA-QA-A7B7 TCGA-RC-A6M4 
       11.87        37.71        13.97        16.67         3.09         0.72 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MC TCGA-ZP-A9CV TCGA-ZP-A9D2 
       19.33        15.39        15.52        16.44        35.77        25.15 
TCGA-ZS-A9CF 
       79.30 

$`XQ LOSS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A3A8 
       83.24        38.40         8.61        69.57        36.66         0.36 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL 
       90.28        26.83        21.17        18.90        23.64         9.96 
TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG 
       22.62         8.12         6.38        81.73        30.74        22.13 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V 
        1.84        20.75         2.14        12.72        24.56        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-2Y-A9GT TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       29.52         0.69        53.39        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
      120.82        40.41        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        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-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-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
        1.12        44.42         0.26        22.36        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       18.48        44.81        13.45         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-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH 
       10.36        11.93        11.41         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-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        13.78        30.61        32.52        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-A73C 
       12.26         0.30        80.75        78.84        23.93        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       12.00         6.41        69.11         0.30         3.52        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       13.64        14.20        51.35         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB 
       18.54        21.63        42.58        22.09        40.54        40.83 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR 
       34.49         0.39        29.52        14.89        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 
       15.58        18.21        18.25        18.15        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK 
        4.64        23.74        15.72        26.63        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       90.48        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        60.99 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       53.69        26.93        28.08        13.91        13.35         9.73 
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-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       14.40        60.89        23.97        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.39        13.68        51.06        53.79        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-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-A7M6 TCGA-G3-A7M7 
       25.25        22.95        20.42        17.10        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 
       14.14        15.78        11.80        13.55        11.64         2.14 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RG TCGA-K7-A6G5 
       28.90         1.02         2.20         2.99        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G 
       11.80        27.25        29.79        12.03         9.57        22.95 
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-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RG-A7D4 
       21.01         0.49         0.30        21.04        19.04        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       27.88        19.76         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       30.41        22.78        13.55        25.71        23.21        35.87 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       12.99        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 
            19.30             19.99 
[1] "0.2 - 83.6 (19.3)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1"  
D82V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ LOSS MUTATED        33       20         0         10          2          2
  XQ LOSS WILD-TYPE     140       67         3         52          7          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ LOSS MUTATED          0         0         0
  XQ LOSS WILD-TYPE        2         1         2
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 33               140
  STAGE II                20                67
  STAGE III                0                 3
  STAGE IIIA              10                52
  STAGE IIIB               2                 7
  STAGE IIIC               2                 5
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED    35  23  13   2
  XQ LOSS WILD-TYPE 148  72  64  10
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              35               148
  T2              23                72
  T3              13                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"
D82V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    50   1
  XQ LOSS WILD-TYPE 204   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     50    1
  XQ LOSS WILD-TYPE  204    2
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              50               204
  1               1                 2
[1] 2 2
[1] FALSE
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    57   0
  XQ LOSS WILD-TYPE 209   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     57    0
  XQ LOSS WILD-TYPE  209    4
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              57               209
  1               0                 4
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    16  58
  XQ LOSS WILD-TYPE 102 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     16   58
  XQ LOSS WILD-TYPE  102  194
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              16               102
  MALE                58               194
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    70   2
  XQ LOSS WILD-TYPE 268   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     70    2
  XQ LOSS WILD-TYPE  268    7
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               70               268
  YES               2                 7
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XQ LOSS MUTATED                         0                       71
  XQ LOSS WILD-TYPE                       3                      289
                   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                 3
  HEPATOCELLULAR CARCINOMA                      71               289
  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    68   2   0   4
  XQ LOSS WILD-TYPE 256  15   1  17
D82V10, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              68               256
  R1               2                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
  XQ LOSS MUTATED                                  0    41
  XQ LOSS WILD-TYPE                                2   117
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           2    30
  XQ LOSS WILD-TYPE                        15   153
D82V11, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                         41               117
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                         30               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"
D82V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  68
  XQ LOSS WILD-TYPE  14 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   68
  XQ LOSS WILD-TYPE   14  267
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              68               267
[1] 2 2
[1] FALSE
