[1] "ofn"        "-oTSTAD-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/STAD-TP/22507291/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/22533931/transformed.cor.cli.txt"

nPatients in clinical file=443, in cluster file=441, common to both=441
[1] "Reduce the number of clustering variables from 82 to 81."
[1]  81 441
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               391 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               391 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              105               336 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              105               336 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               78               363 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               78               363 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               66               375 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               66               375 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               52               389 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               52               389 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               91               350 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               91               350 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               21               420 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               21               420 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               425 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               425 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              100               341 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              100               341 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               43               398 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               43               398 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               81               360 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               81               360 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               66               375 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               66               375 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              202               239 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              202               239 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              171               270 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              171               270 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              183               258 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              183               258 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              240               201 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              240               201 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               59               382 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               59               382 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               77               364 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               77               364 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                98                343 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                98                343 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                67                374 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                67                374 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                62                379 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                62                379 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                74                367 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                74                367 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                92                349 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                92                349 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                78                363 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                78                363 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               153                288 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               153                288 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                28                413 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                28                413 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                39                402 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                39                402 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                58                383 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                58                383 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                48                393 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                48                393 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                29                412 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                29                412 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                64                377 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                64                377 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                85                356 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                85                356 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                55                386 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                55                386 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                53                388 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                53                388 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                79                362 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                79                362 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               242                199 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               242                199 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               280                161 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               280                161 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                22                419 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                22                419 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                32                409 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                32                409 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               51               390 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               51               390 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               55               386 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               55               386 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               58               383 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               58               383 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               416 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               416 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               23               418 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               23               418 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               30               411 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               30               411 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               93               348 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               93               348 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               56               385 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               56               385 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              167               274 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              167               274 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              165               276 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              165               276 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               63               378 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               63               378 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              108               333 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              108               333 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               50               391 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               50               391 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               69               372 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               69               372 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               17               424 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               17               424 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               29               412 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               29               412 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               91               350 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               91               350 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               37               404 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               37               404 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              149               292 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              149               292 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              104               337 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              104               337 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                64                377 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                64                377 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                68                373 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                68                373 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                64                377 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                64                377 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                61                380 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                61                380 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                62                379 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                62                379 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                52                389 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                52                389 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                37                404 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                37                404 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               111                330 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               111                330 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                90                351 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                90                351 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               100                341 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               100                341 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               114                327 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               114                327 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               164                277 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               164                277 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                74                367 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                74                367 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               119                322 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               119                322 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               154                287 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               154                287 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               116                325 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               116                325 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                86                355 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                86                355 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                22                419 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                22                419 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               181                260 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               181                260 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               146                295 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               146                295 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               61               380 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               61               380 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               55               386 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               55               386 
[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] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 441 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=152,	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=225,	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=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=7,	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=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=33,	numeric=TRUE,	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 441 columns, 1 survival variables, and 12 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] "NUMBER_OF_LYMPH_NODES" "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=54, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 23  93 196 119 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 23  93 196 119 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 23  93 196 119 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 23  93 196 119 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
130 119  86  88 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
130 119  86  88 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
130 119  86  88 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
130 119  86  88 
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=7, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=33, binary=FALSE, numeric=TRUE
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    23  21
  1P GAIN WILD-TYPE 223 148
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               44               371 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               21               148 
$`1P GAIN MUTATED`
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8381 
        9.67         6.18        18.15         3.45        29.42         7.36 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4J8 
        5.39        25.18        12.79         8.22         0.72        13.51 
TCGA-CD-8535 TCGA-CD-A48A TCGA-CG-4436 TCGA-D7-6521 TCGA-D7-A4YU TCGA-D7-A6F0 
       12.82        12.43         7.99        18.54        16.44        22.29 
TCGA-EQ-8122 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
        7.99        26.47         5.92         3.25        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RR 
        6.58        12.95         3.45        18.38         6.44         6.74 
TCGA-KB-A6F7 TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DU 
       63.62         6.08        16.67       115.69         8.94         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PK TCGA-VQ-A8PZ TCGA-VQ-A94R TCGA-VQ-A94T 
       18.48        43.36        17.85        73.41        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA6A 
       18.41        38.93 

$`1P GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 
       20.15         9.86        27.35        26.93        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 
       11.80        31.27        14.79        25.05         3.72         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        12.30        11.31        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       26.43        11.24        11.31        11.44        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       24.20        22.75        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51        20.25         0.26         2.10        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
       18.81         3.39        12.46        13.35        19.53        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 
        5.79         0.92        48.79        13.25        13.02        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.72              0.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           115.69            122.30 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           12.805            15.320 
[1] "0.7 - 115.7 (12.8)" "0.0 - 122.3 (15.3)"
[1] "hr=" "1.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         1        2        7        2         3         5
  1P GAIN WILD-TYPE       1       14       34       30        37        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           1          8          9          5        1
  1P GAIN WILD-TYPE         2         73         54         34       43
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 2                14
  STAGE IB                 7                34
  STAGE II                 2                30
  STAGE IIA                3                37
  STAGE IIB                5                51
  STAGE III                1                 2
  STAGE IIIA               8                73
  STAGE IIIB               9                54
  STAGE IIIC               5                34
  STAGE IV                 1                43
[1] 11  2
[1] 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     5   8  25  10
  1P GAIN WILD-TYPE  18  85 171 109
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               5                18
  T2               8                85
  T3              25               171
  T4              10               109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P GAIN MUTATED    15  10  12   9
  1P GAIN WILD-TYPE 115 109  74  79
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              15               115
  N1              10               109
  N2              12                74
  N3               9                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    46   1
  1P GAIN WILD-TYPE 343  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     46    1
  1P GAIN WILD-TYPE  343   29
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              46               343
  1               1                29
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    14  36
  1P GAIN WILD-TYPE 144 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     14   36
  1P GAIN WILD-TYPE  144  247
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              14               144
  MALE                36               247
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    34  12
  1P GAIN WILD-TYPE 288  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     34   12
  1P GAIN WILD-TYPE  288   64
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               34               288
  YES              12                64
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  1P GAIN MUTATED                                          2
  1P GAIN WILD-TYPE                                       11
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  1P GAIN MUTATED                                       7
  1P GAIN WILD-TYPE                                    65
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                       22
  1P GAIN WILD-TYPE                                                    141
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  1P GAIN MUTATED                                                   0
  1P GAIN WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                                  11
  1P GAIN WILD-TYPE                                                                71
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  1P GAIN MUTATED                                                    0
  1P GAIN WILD-TYPE                                                  8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  1P GAIN MUTATED                                                  8
  1P GAIN WILD-TYPE                                               71
D1V9, multiclass
                                                                   clus
vv                                                                  1P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              11
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                8
                                                                   clus
vv                                                                  1P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                71
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 71
[1] 7 2
[1] TRUE
[1] "dimension of 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    40   2   0   4
  1P GAIN WILD-TYPE 309  16  19  21
D1V10, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              40               309
  R1               2                16
  R2               0                19
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1P GAIN MUTATED      11                         2
  1P GAIN WILD-TYPE    77                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           0    34
  1P GAIN WILD-TYPE                                         1   244
D1V12, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  34               244
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  39
  1P GAIN WILD-TYPE   5 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   39
  1P GAIN WILD-TYPE    5  277
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              39               277
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    56  41
  1Q GAIN WILD-TYPE 190 128
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               97               318 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               41               128 
$`1Q GAIN MUTATED`
TCGA-CG-4460 TCGA-VQ-A94U TCGA-B7-A5TJ TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
       21.99        26.93        11.01         4.08         9.67         6.18 
TCGA-BR-6705 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8295 
       25.61        18.15        28.73         3.45        29.42         2.20 
TCGA-BR-8360 TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        6.18        14.04         7.36         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A452 
       20.22         1.12        12.79        31.96         8.22         7.53 
TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-8524 
        0.72        28.34        13.51        20.42         1.15        12.76 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CG-4436 
       12.39        15.39        12.82        11.61         6.58         7.99 
TCGA-CG-4438 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 
       54.08        12.66        20.91        18.54        17.19        10.26 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        24.72        19.50 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
       16.44        11.31        22.29         0.62         7.99        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7134 
        3.48        14.07        13.58         0.56         5.52        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-A4GC 
       30.51        26.47         5.92        24.39        28.96         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-7808 
       25.81        11.77         0.10         6.58        12.95         3.45 
TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 
        6.44        63.62        18.21         6.08        16.67       115.69 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        8.94        35.61        48.79         5.46        18.48        43.36 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91S 
        2.70        17.85        14.33        73.41        39.45        32.88 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A 
       66.81        21.04        42.54        11.24        18.41        38.93 
TCGA-VQ-AA6K 
       12.43 

$`1Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.86        27.35        58.03        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 
       18.35        30.90         4.08         9.34         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       39.78        15.32         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56         2.66        19.96        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       25.05         3.72        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        34.13        13.87         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        32.52         0.46        20.65        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       11.21        12.10        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 
       12.30        12.59        11.64        12.07        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        11.31        12.43        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        25.71        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8572 
       18.61        17.85        13.35        15.22        15.98        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 
        7.13        14.47        21.27        11.38        19.53        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       17.06        59.54         5.03         6.21        77.29        63.06 
TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        1.51        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68        24.20        22.75 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         8.98         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV 
       57.44        16.87        19.04         5.79         0.92        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.02        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       12.79         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       29.59        64.57        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       20.81         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
        5.72         2.66        43.66        28.41        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        27.55        17.26         0.79 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              0.1               0.0 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           115.69            122.30 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           13.510            15.615 
[1] "0.1 - 115.7 (13.5)" "0.0 - 122.3 (15.6)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         0        6       11        7         6        11
  1Q GAIN WILD-TYPE       2       10       30       25        34        45
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           1         20         18         11        6
  1Q GAIN WILD-TYPE         2         61         45         28       38
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 6                10
  STAGE IB                11                30
  STAGE II                 7                25
  STAGE IIA                6                34
  STAGE IIB               11                45
  STAGE III                1                 2
  STAGE IIIA              20                61
  STAGE IIIB              18                45
  STAGE IIIC              11                28
  STAGE IV                 6                38
[1] 11  2
[1] 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     7  20  48  28
  1Q GAIN WILD-TYPE  16  73 148  91
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               7                16
  T2              20                73
  T3              48               148
  T4              28                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED    30  19  26  23
  1Q GAIN WILD-TYPE 100 100  60  65
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              30               100
  N1              19               100
  N2              26                60
  N3              23                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    93   5
  1Q GAIN WILD-TYPE 296  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     93    5
  1Q GAIN WILD-TYPE  296   25
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              93               296
  1               5                25
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    34  71
  1Q GAIN WILD-TYPE 124 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     34   71
  1Q GAIN WILD-TYPE  124  212
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              34               124
  MALE                71               212
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    73  24
  1Q GAIN WILD-TYPE 249  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     73   24
  1Q GAIN WILD-TYPE  249   52
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               73               249
  YES              24                52
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  1Q GAIN MUTATED                                          5
  1Q GAIN WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  1Q GAIN MUTATED                                      12
  1Q GAIN WILD-TYPE                                    60
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                       36
  1Q GAIN WILD-TYPE                                                    127
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  1Q GAIN MUTATED                                                   4
  1Q GAIN WILD-TYPE                                                17
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                                  20
  1Q GAIN WILD-TYPE                                                                62
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  1Q GAIN MUTATED                                                    1
  1Q GAIN WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  1Q GAIN MUTATED                                                 27
  1Q GAIN WILD-TYPE                                               52
D2V9, multiclass
                                                                   clus
vv                                                                  1Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         36
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              20
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               27
                                                                   clus
vv                                                                  1Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          127
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 52
[1] 7 2
[1] TRUE
[1] "dimension of 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    80   7   3   7
  1Q GAIN WILD-TYPE 269  11  16  18
D2V10, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              80               269
  R1               7                11
  R2               3                16
  RX               7                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"
D2V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1Q GAIN MUTATED      23                         6
  1Q GAIN WILD-TYPE    65                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           0    67
  1Q GAIN WILD-TYPE                                         1   211
D2V12, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                                  23                65
  BLACK OR AFRICAN AMERICAN                               6                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  67               211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     0  81
  1Q GAIN WILD-TYPE   5 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   81
  1Q GAIN WILD-TYPE    5  235
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              81               235
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    48  24
  2P GAIN WILD-TYPE 198 145
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               72               343 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               24               145 
$`2P GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-MX-A663 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-6456 
       21.99        79.07         9.86        11.01         6.61        17.29 
TCGA-BR-6566 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8077 
       32.78         9.21        35.24        33.63        18.15         0.69 
TCGA-BR-8080 TCGA-BR-8295 TCGA-BR-8362 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        9.60         2.20        13.08         5.39         9.21        20.22 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5800 
        1.48        12.89        13.51        20.65        20.42        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 
       13.18        13.35        12.76        12.00        36.00        12.03 
TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F2 
       18.54        15.98        18.21        16.44        11.24        15.65 
TCGA-FP-A9TM TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GD 
        6.21        28.96         0.76        24.30        24.26        22.75 
TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
       25.81         8.98         6.58         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 
       23.80        33.40         3.45        12.59        10.62         5.56 
TCGA-KB-A93H TCGA-R5-A7ZE TCGA-RD-A8N6 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PE 
       37.64        18.21         8.94        43.36        21.73        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-AA68 
       12.79        17.85        20.81         1.71        66.81        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       38.93        32.94        16.14        27.55        17.26         0.79 

$`2P GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       47.05        22.98        16.24         0.23        20.15        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       26.93        58.03        26.70        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       21.90        36.16        35.84        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44        29.59        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96        15.58         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.05         3.72        25.18         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08        34.98        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        32.52         0.46         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 
        5.13        13.41        13.02        11.21        12.10        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.84        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       12.33        24.72        16.80        19.50        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.31        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         5.52        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        18.15        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       22.82        21.07         5.59        22.68        24.20         3.25 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        21.37        29.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        0.26        29.00        21.17        14.07        15.68        36.36 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.44         6.74         6.51        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        18.48        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        61.22        18.74        32.88        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58         5.72        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       11.24        18.41        28.41        17.13        54.12        26.04 
TCGA-VQ-AA6K 
       12.43 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.69              0.00 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            79.07            122.30 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            16.06             14.66 
[1] "0.7 - 79.1 (16.1)"  "0.0 - 122.3 (14.7)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         0        5        6        7         7        13
  2P GAIN WILD-TYPE       2       11       35       25        33        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           0         10         11          9        6
  2P GAIN WILD-TYPE         3         71         52         30       38
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 5                11
  STAGE IB                 6                35
  STAGE II                 7                25
  STAGE IIA                7                33
  STAGE IIB               13                43
  STAGE III                0                 3
  STAGE IIIA              10                71
  STAGE IIIB              11                52
  STAGE IIIC               9                30
  STAGE IV                 6                38
[1] 11  2
[1] 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     6  13  39  19
  2P GAIN WILD-TYPE  17  80 157 100
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               6                17
  T2              13                80
  T3              39               157
  T4              19               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P GAIN MUTATED    26  16  15  19
  2P GAIN WILD-TYPE 104 103  71  69
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              26               104
  N1              16               103
  N2              15                71
  N3              19                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    72   4
  2P GAIN WILD-TYPE 317  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     72    4
  2P GAIN WILD-TYPE  317   26
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              72               317
  1               4                26
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    29  49
  2P GAIN WILD-TYPE 129 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     29   49
  2P GAIN WILD-TYPE  129  234
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              29               129
  MALE                49               234
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    64   9
  2P GAIN WILD-TYPE 258  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     64    9
  2P GAIN WILD-TYPE  258   67
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               64               258
  YES               9                67
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  2P GAIN MUTATED                                          0
  2P GAIN WILD-TYPE                                       13
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  2P GAIN MUTATED                                       9
  2P GAIN WILD-TYPE                                    63
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                       26
  2P GAIN WILD-TYPE                                                    137
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  2P GAIN MUTATED                                                   1
  2P GAIN WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                                  18
  2P GAIN WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  2P GAIN MUTATED                                                    3
  2P GAIN WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  2P GAIN MUTATED                                                 20
  2P GAIN WILD-TYPE                                               59
D3V9, multiclass
                                                                   clus
vv                                                                  2P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         26
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               20
                                                                   clus
vv                                                                  2P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         13
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          137
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of 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    68   1   3   2
  2P GAIN WILD-TYPE 281  17  16  23
D3V10, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              68               281
  R1               1                17
  R2               3                16
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2P GAIN MUTATED      22                         1
  2P GAIN WILD-TYPE    66                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           0    46
  2P GAIN WILD-TYPE                                         1   232
D3V12, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                                  22                66
  BLACK OR AFRICAN AMERICAN                               1                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  46               232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  56
  2P GAIN WILD-TYPE   5 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   56
  2P GAIN WILD-TYPE    5  260
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              56               260
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    38  23
  2Q GAIN WILD-TYPE 208 146
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               61               354 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               23               146 
$`2Q GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-MX-A663 TCGA-B7-A5TJ TCGA-BR-6456 TCGA-BR-6566 
       21.99        79.07         9.86        11.01        17.29        32.78 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8077 TCGA-BR-8080 
        9.21        35.24        33.63        18.15         0.69         9.60 
TCGA-BR-8295 TCGA-BR-8362 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-A4CS TCGA-BR-A4IY 
        2.20        13.08         5.39         9.21         1.48        12.89 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-A48C 
        0.66        13.51        20.42        13.18        12.76        11.61 
TCGA-CG-5718 TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-A4YU TCGA-D7-A6EV 
       36.00        12.03        18.54        15.98        16.44        11.24 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-A9TM TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
        7.99        72.23         6.21         0.76        24.30        24.26 
TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       25.81         6.58         2.10        12.95        23.84        23.80 
TCGA-IN-7808 TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A93H TCGA-RD-A8N6 
        3.45        12.59        10.62         5.56        37.64         8.94 
TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A91U 
       43.36        22.19        12.79        17.85        20.81         1.71 
TCGA-VQ-A92D TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       66.81        38.93        32.94        16.14        27.55        17.26 
TCGA-ZQ-A9CR 
        0.79 

$`2Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       47.05        22.98        16.24         0.23        20.15        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       26.93        58.03        26.70        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       44.94        21.90        36.16        35.84        39.78        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44        29.59        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
        7.36        25.05         3.72        25.18        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       34.98        27.55        28.57         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF 
        0.53        28.34        32.52         0.46        20.65         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.35        11.21        12.10        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       21.07         5.59        22.68        24.20         3.25        22.75 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       20.25         0.26        29.00        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40        36.36        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU 
       13.35        19.53         6.44         6.74         6.51        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        0.92        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       34.29        46.26        16.31         2.50         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        32.88        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       43.66        28.41        17.13        54.12        26.04        12.43 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.66              0.00 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            79.07            122.30 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            13.18             15.12 
[1] "0.7 - 79.1 (13.2)"  "0.0 - 122.3 (15.1)"
[1] "hr=" "1"  
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         0        4        5        5         6        13
  2Q GAIN WILD-TYPE       2       12       36       27        34        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           0          5         11          7        5
  2Q GAIN WILD-TYPE         3         76         52         32       39
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 4                12
  STAGE IB                 5                36
  STAGE II                 5                27
  STAGE IIA                6                34
  STAGE IIB               13                43
  STAGE III                0                 3
  STAGE IIIA               5                76
  STAGE IIIB              11                52
  STAGE IIIC               7                32
  STAGE IV                 5                39
[1] 11  2
[1] 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     4  12  34  15
  2Q GAIN WILD-TYPE  19  81 162 104
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               4                19
  T2              12                81
  T3              34               162
  T4              15               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"
                   vv
clus                 N0  N1  N2  N3
  2Q GAIN MUTATED    21  14  11  17
  2Q GAIN WILD-TYPE 109 105  75  71
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              21               109
  N1              14               105
  N2              11                75
  N3              17                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    58   4
  2Q GAIN WILD-TYPE 331  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     58    4
  2Q GAIN WILD-TYPE  331   26
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              58               331
  1               4                26
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    25  41
  2Q GAIN WILD-TYPE 133 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     25   41
  2Q GAIN WILD-TYPE  133  242
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              25               133
  MALE                41               242
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    54   7
  2Q GAIN WILD-TYPE 268  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     54    7
  2Q GAIN WILD-TYPE  268   69
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               54               268
  YES               7                69
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  2Q GAIN MUTATED                                          0
  2Q GAIN WILD-TYPE                                       13
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  2Q GAIN MUTATED                                       7
  2Q GAIN WILD-TYPE                                    65
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                       25
  2Q GAIN WILD-TYPE                                                    138
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  2Q GAIN MUTATED                                                   1
  2Q GAIN WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                                  18
  2Q GAIN WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  2Q GAIN MUTATED                                                    2
  2Q GAIN WILD-TYPE                                                  6
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  2Q GAIN MUTATED                                                 13
  2Q GAIN WILD-TYPE                                               66
D4V9, multiclass
                                                                   clus
vv                                                                  2Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         25
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               13
                                                                   clus
vv                                                                  2Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         13
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          138
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 66
[1] 7 2
[1] TRUE
[1] "dimension of 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    56   1   3   2
  2Q GAIN WILD-TYPE 293  17  16  23
D4V10, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              56               293
  R1               1                17
  R2               3                16
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2Q GAIN MUTATED      16                         2
  2Q GAIN WILD-TYPE    72                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           0    41
  2Q GAIN WILD-TYPE                                         1   237
D4V12, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                                  16                72
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  41               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  48
  2Q GAIN WILD-TYPE   5 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   48
  2Q GAIN WILD-TYPE    5  268
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              48               268
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    32  17
  3P GAIN WILD-TYPE 214 152
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               49               366 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17               152 
$`3P GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-5727 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6565 
       47.05        79.07         9.67         6.18        34.68         9.17 
TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-8296 TCGA-BR-8373 
       30.90        21.90        15.32         3.45        15.58        14.79 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8528 TCGA-CG-4477 
       32.52        20.65        13.02        13.18        12.33        30.97 
TCGA-CG-5724 TCGA-D7-6815 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-F1-A448 
       12.03        15.98        16.44        11.24        22.29        21.27 
TCGA-FP-7998 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 
       22.29        24.20        25.81         8.98         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-R5-A7ZR TCGA-RD-A8N1 TCGA-RD-A8N9 
       29.00        23.80        33.40         6.08       115.69        35.61 
TCGA-VQ-A8DT TCGA-VQ-A8P5 TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PX 
       48.79         7.73        17.85        23.41        13.35        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A94O 
       73.41        21.83         9.73         9.04         2.01        21.04 
TCGA-VQ-AA6F 
       54.12 

$`3P GAIN WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        22.98        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       27.35        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       18.15        28.73         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        28.34         0.66        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        1.15        21.44        16.14         5.13        13.41        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.31        11.44        20.32 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       14.07        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.26        22.68         3.25        22.75        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.84        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       15.75        13.51         2.53         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        5.13        16.67       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        0.92         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91A 
        1.87         9.27        15.65        29.59        14.33        39.45 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 
       42.64        60.85         9.50        55.56        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58         5.72        66.81         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2.01              0.00 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           115.69            122.30 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            20.65             14.22 
[1] "2.0 - 115.7 (20.6)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         0        2        5        4         4         8
  3P GAIN WILD-TYPE       2       14       36       28        36        48
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           1          8          7          7        5
  3P GAIN WILD-TYPE         2         73         56         32       39
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                14
  STAGE IB                 5                36
  STAGE II                 4                28
  STAGE IIA                4                36
  STAGE IIB                8                48
  STAGE III                1                 2
  STAGE IIIA               8                73
  STAGE IIIB               7                56
  STAGE IIIC               7                32
  STAGE IV                 5                39
[1] 11  2
[1] 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     2  11  22  16
  3P GAIN WILD-TYPE  21  82 174 103
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               2                21
  T2              11                82
  T3              22               174
  T4              16               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P GAIN MUTATED    16  12   8  13
  3P GAIN WILD-TYPE 114 107  78  75
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              16               114
  N1              12               107
  N2               8                78
  N3              13                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    49   2
  3P GAIN WILD-TYPE 340  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     49    2
  3P GAIN WILD-TYPE  340   28
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              49               340
  1               2                28
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    20  32
  3P GAIN WILD-TYPE 138 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     20   32
  3P GAIN WILD-TYPE  138  251
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              20               138
  MALE                32               251
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    38  11
  3P GAIN WILD-TYPE 284  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     38   11
  3P GAIN WILD-TYPE  284   65
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               38               284
  YES              11                65
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  3P GAIN MUTATED                                          1
  3P GAIN WILD-TYPE                                       12
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  3P GAIN MUTATED                                       9
  3P GAIN WILD-TYPE                                    63
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                       14
  3P GAIN WILD-TYPE                                                    149
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  3P GAIN MUTATED                                                   2
  3P GAIN WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                                  13
  3P GAIN WILD-TYPE                                                                69
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  3P GAIN MUTATED                                                    1
  3P GAIN WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  3P GAIN MUTATED                                                 12
  3P GAIN WILD-TYPE                                               67
D5V9, multiclass
                                                                   clus
vv                                                                  3P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              13
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               12
                                                                   clus
vv                                                                  3P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                69
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 67
[1] 7 2
[1] TRUE
[1] "dimension of 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    43   2   2   3
  3P GAIN WILD-TYPE 306  16  17  22
D5V10, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              43               306
  R1               2                16
  R2               2                17
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED      13                         2
  3P GAIN WILD-TYPE    75                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           0    28
  3P GAIN WILD-TYPE                                         1   250
D5V12, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                                  13                75
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  28               250
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  32
  3P GAIN WILD-TYPE   3 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   32
  3P GAIN WILD-TYPE    3  284
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              32               284
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    52  34
  3Q GAIN WILD-TYPE 194 135
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               86               329 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               34               135 
$`3Q GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-5727 TCGA-VQ-A8PU TCGA-B7-5818 TCGA-BR-4257 TCGA-BR-4267 
       47.05        79.07        27.35        11.70         9.67         6.18 
TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 TCGA-BR-7723 
       34.68         9.17        30.90        21.90        15.32        28.73 
TCGA-BR-7901 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8367 
        3.45         8.05         2.20        15.58        31.10        26.33 
TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-A4J4 TCGA-BR-A4J7 
       14.79        25.18        12.79        27.12         0.53        32.52 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8527 
       20.65        20.42        13.02        13.18        11.21         7.17 
TCGA-CD-8528 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4477 
       12.33        15.95         7.99        12.03        12.00        30.97 
TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-A4YU TCGA-D7-A6EV 
       12.03        18.54        15.98        24.72        16.44        11.24 
TCGA-D7-A6F0 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-HU-A4G6 
       22.29        21.27        14.07        22.29        26.47        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 
       24.20        22.75        25.81         8.98         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4HD TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F7 
       29.00        33.40         6.44        10.62        11.70        63.62 
TCGA-R5-A7ZR TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DZ 
        6.08        37.91       115.69        35.61        48.79        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       18.48        43.36        21.73         7.73         2.70        17.85 
TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Y 
       23.41        13.35        64.57        73.41        21.83         9.73 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA6A TCGA-VQ-AA6F 
        9.04         2.01         4.54        21.04        38.93        54.12 
TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       27.55         0.79 

$`3Q GAIN WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        22.98        16.24         0.23        20.15         9.86 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       26.93        58.03        26.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         4.08         9.34         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 
        8.98        40.21        31.20        44.94         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7957 
       35.24        35.84        33.63        39.78        18.15         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       19.96         7.40         6.18        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
       31.27         7.36        25.05         3.72         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22         1.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.72        14.17        28.34         0.66        13.51         0.46 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        1.15        21.44        16.14         5.13        13.41        13.15 
TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 
       13.35        12.10        12.76        12.59        12.53        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07         0.00         9.01        18.97         7.07 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        12.79        12.36        11.31        12.33 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.31        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 
       72.23        11.38         3.48        19.53        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.30         5.59        22.68         3.25        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        23.80        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
       19.53         6.74        12.59         6.51        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       14.04        45.67        18.21         8.52        74.53         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E7 
       19.04         5.79         0.92         5.46        13.25        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       22.19         2.50        12.79         1.87         9.27        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N 
       29.59        14.33        39.45        11.70        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.56        55.43         6.58         5.72        66.81         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B 
       42.54        11.24        18.41        43.66        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        26.04        16.14        12.43        17.26 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.53              0.00 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           115.69            122.30 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           18.165            14.170 
[1] "0.5 - 115.7 (18.2)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         0        3       10        8         5        12
  3Q GAIN WILD-TYPE       2       13       31       24        35        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           1         12         16         13        8
  3Q GAIN WILD-TYPE         2         69         47         26       36
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                13
  STAGE IB                10                31
  STAGE II                 8                24
  STAGE IIA                5                35
  STAGE IIB               12                44
  STAGE III                1                 2
  STAGE IIIA              12                69
  STAGE IIIB              16                47
  STAGE IIIC              13                26
  STAGE IV                 8                36
[1] 11  2
[1] 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     5  19  35  31
  3Q GAIN WILD-TYPE  18  74 161  88
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               5                18
  T2              19                74
  T3              35               161
  T4              31                88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q GAIN MUTATED    25  22  17  23
  3Q GAIN WILD-TYPE 105  97  69  65
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              25               105
  N1              22                97
  N2              17                69
  N3              23                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    81   4
  3Q GAIN WILD-TYPE 308  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     81    4
  3Q GAIN WILD-TYPE  308   26
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              81               308
  1               4                26
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    33  58
  3Q GAIN WILD-TYPE 125 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     33   58
  3Q GAIN WILD-TYPE  125  225
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              33               125
  MALE                58               225
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    67  19
  3Q GAIN WILD-TYPE 255  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     67   19
  3Q GAIN WILD-TYPE  255   57
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               67               255
  YES              19                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  3Q GAIN MUTATED                                          3
  3Q GAIN WILD-TYPE                                       10
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  3Q GAIN MUTATED                                      12
  3Q GAIN WILD-TYPE                                    60
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                       30
  3Q GAIN WILD-TYPE                                                    133
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  3Q GAIN MUTATED                                                   3
  3Q GAIN WILD-TYPE                                                18
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                                  22
  3Q GAIN WILD-TYPE                                                                60
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  3Q GAIN MUTATED                                                    1
  3Q GAIN WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  3Q GAIN MUTATED                                                 19
  3Q GAIN WILD-TYPE                                               60
D6V9, multiclass
                                                                   clus
vv                                                                  3Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         30
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              22
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               19
                                                                   clus
vv                                                                  3Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of 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    76   2   5   4
  3Q GAIN WILD-TYPE 273  16  14  21
D6V10, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              76               273
  R1               2                16
  R2               5                14
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED      19                         5
  3Q GAIN WILD-TYPE    69                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           0    51
  3Q GAIN WILD-TYPE                                         1   227
D6V12, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                                  19                69
  BLACK OR AFRICAN AMERICAN                               5                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  51               227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     2  56
  3Q GAIN WILD-TYPE   3 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   56
  3Q GAIN WILD-TYPE    3  260
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              56               260
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    14   7
  4P GAIN WILD-TYPE 232 162
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               21               394 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                7               162 
$`4P GAIN MUTATED`
TCGA-CG-4475 TCGA-VQ-A8PU TCGA-BR-8484 TCGA-BR-A4IY TCGA-CD-8528 TCGA-CG-4443 
       22.98        27.35        25.18        12.89        12.33        29.98 
TCGA-CG-5720 TCGA-CG-5722 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-A6EV TCGA-D7-A6F2 
        0.99         0.99        12.66        20.91        11.24        15.65 
TCGA-HU-8610 TCGA-HU-A4GH TCGA-IN-7806 TCGA-IN-A7NT TCGA-VQ-A8PM TCGA-VQ-A8PS 
        0.76        11.77        36.36        10.62         1.87        13.35 
TCGA-VQ-A91Q TCGA-VQ-A92D TCGA-VQ-AA6K 
       20.81        66.81        12.43 

$`4P GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.86        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        34.98         1.48        27.55        28.57         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08         4.01        14.01        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
        6.97        36.00         1.02         6.02       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        7.99        25.71        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.31        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       30.51        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.32        22.82        21.07        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       23.80        21.17        14.07        15.68        33.40         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
        6.44         6.74        12.59         6.51        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO 
       22.19         2.50        12.79         2.70        17.85         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        17.26         0.79 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.76              0.00 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            66.81            122.30 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            12.89             15.12 
[1] "0.8 - 66.8 (12.9)"  "0.0 - 122.3 (15.1)"
[1] "hr=" "1.1"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         0        3        3        0         0         5
  4P GAIN WILD-TYPE       2       13       38       32        40        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           0          6          0          1        3
  4P GAIN WILD-TYPE         3         75         63         38       41
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                13
  STAGE IB                 3                38
  STAGE II                 0                32
  STAGE IIA                0                40
  STAGE IIB                5                51
  STAGE III                0                 3
  STAGE IIIA               6                75
  STAGE IIIB               0                63
  STAGE IIIC               1                38
  STAGE IV                 3                41
[1] 11  2
[1] 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     3   4   8   6
  4P GAIN WILD-TYPE  20  89 188 113
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               3                20
  T2               4                89
  T3               8               188
  T4               6               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P GAIN MUTATED     8   6   4   3
  4P GAIN WILD-TYPE 122 113  82  85
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               8               122
  N1               6               113
  N2               4                82
  N3               3                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"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    20   1
  4P GAIN WILD-TYPE 369  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     20    1
  4P GAIN WILD-TYPE  369   29
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              20               369
  1               1                29
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     5  16
  4P GAIN WILD-TYPE 153 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5   16
  4P GAIN WILD-TYPE  153  267
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               5               153
  MALE                16               267
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    14   4
  4P GAIN WILD-TYPE 308  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     14    4
  4P GAIN WILD-TYPE  308   72
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               14               308
  YES               4                72
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  4P GAIN MUTATED                                          2
  4P GAIN WILD-TYPE                                       11
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  4P GAIN MUTATED                                       1
  4P GAIN WILD-TYPE                                    71
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                        6
  4P GAIN WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  4P GAIN MUTATED                                                   1
  4P GAIN WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                                   3
  4P GAIN WILD-TYPE                                                                79
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  4P GAIN MUTATED                                                    0
  4P GAIN WILD-TYPE                                                  8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  4P GAIN MUTATED                                                  7
  4P GAIN WILD-TYPE                                               72
D7V9, multiclass
                                                                   clus
vv                                                                  4P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                7
                                                                   clus
vv                                                                  4P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            71
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                79
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 72
[1] 7 2
[1] TRUE
[1] "dimension of 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    18   2   1   0
  4P GAIN WILD-TYPE 331  16  18  25
D7V10, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              18               331
  R1               2                16
  R2               1                18
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4P GAIN MUTATED       4                         0
  4P GAIN WILD-TYPE    84                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0    12
  4P GAIN WILD-TYPE                                         1   266
D7V12, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                                   4                84
  BLACK OR AFRICAN AMERICAN                               0                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               266
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  11
  4P GAIN WILD-TYPE   5 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   11
  4P GAIN WILD-TYPE    5  305
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              11               305
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     8   8
  4Q GAIN WILD-TYPE 238 161
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               399 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               161 
$`4Q GAIN MUTATED`
TCGA-CG-4475 TCGA-VQ-A8PU TCGA-BR-8484 TCGA-CG-5720 TCGA-CG-5722 TCGA-D7-5578 
       22.98        27.35        25.18         0.99         0.99        12.66 
TCGA-D7-A6EV TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8610 TCGA-IN-7806 TCGA-RD-A8N5 
       11.24        26.47        28.96         0.76        36.36        57.44 
TCGA-VQ-A8PM TCGA-VQ-A91Q TCGA-VQ-A92D TCGA-VQ-A94T 
        1.87        20.81        66.81        11.24 

$`4Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.86        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        25.71        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        33.40         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
        2.53         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        0.92        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79         2.70        17.85         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        21.83        61.22        18.74        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
        2.01        55.43         4.54         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        42.54        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.76              0.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            66.81            122.30 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           21.895            14.760 
[1] "0.8 - 66.8 (21.9)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.1"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         0        1        3        0         0         3
  4Q GAIN WILD-TYPE       2       15       38       32        40        53
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           0          5          1          0        3
  4Q GAIN WILD-TYPE         3         76         62         39       41
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                15
  STAGE IB                 3                38
  STAGE II                 0                32
  STAGE IIA                0                40
  STAGE IIB                3                53
  STAGE III                0                 3
  STAGE IIIA               5                76
  STAGE IIIB               1                62
  STAGE IIIC               0                39
  STAGE IV                 3                41
[1] 11  2
[1] 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     1   4   8   3
  4Q GAIN WILD-TYPE  22  89 188 116
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               1                22
  T2               4                89
  T3               8               188
  T4               3               116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q GAIN MUTATED     4   5   5   2
  4Q GAIN WILD-TYPE 126 114  81  86
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               4               126
  N1               5               114
  N2               5                81
  N3               2                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    14   1
  4Q GAIN WILD-TYPE 375  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     14    1
  4Q GAIN WILD-TYPE  375   29
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              14               375
  1               1                29
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4  12
  4Q GAIN WILD-TYPE 154 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4   12
  4Q GAIN WILD-TYPE  154  271
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4               154
  MALE                12               271
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    11   3
  4Q GAIN WILD-TYPE 311  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     11    3
  4Q GAIN WILD-TYPE  311   73
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               11               311
  YES               3                73
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  4Q GAIN MUTATED                                          2
  4Q GAIN WILD-TYPE                                       11
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  4Q GAIN MUTATED                                       2
  4Q GAIN WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                        3
  4Q GAIN WILD-TYPE                                                    160
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  4Q GAIN MUTATED                                                   1
  4Q GAIN WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                                   1
  4Q GAIN WILD-TYPE                                                                81
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  4Q GAIN MUTATED                                                    0
  4Q GAIN WILD-TYPE                                                  8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  4Q GAIN MUTATED                                                  6
  4Q GAIN WILD-TYPE                                               73
D8V9, multiclass
                                                                   clus
vv                                                                  4Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                6
                                                                   clus
vv                                                                  4Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          160
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                81
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 73
[1] 7 2
[1] TRUE
[1] "dimension of 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    15   0   1   0
  4Q GAIN WILD-TYPE 334  18  18  25
D8V10, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              15               334
  R1               0                18
  R2               1                18
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4Q GAIN MUTATED       2                         0
  4Q GAIN WILD-TYPE    86                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0     9
  4Q GAIN WILD-TYPE                                         1   269
D8V12, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                                   2                86
  BLACK OR AFRICAN AMERICAN                               0                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               269
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   8
  4Q GAIN WILD-TYPE   5 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    8
  4Q GAIN WILD-TYPE    5  308
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               8               308
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    57  36
  5P GAIN WILD-TYPE 189 133
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               93               322 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               36               133 
$`5P GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-BR-4187 
       47.05        21.99        22.98         0.23        20.15         4.64 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 
        9.21        35.24        33.63        39.78        18.15         3.45 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
       11.44         0.69         8.05        29.42         2.66        15.58 
TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 
        0.26        17.52        26.33        14.79         9.21        20.22 
TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8525 
       24.79         8.22        20.65        13.18        12.76        12.59 
TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 
       12.33         6.31        11.61         7.99        54.08        14.01 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5722 
       12.03        18.97         7.07        12.00        36.00         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6527 TCGA-D7-6528 
       12.03        15.02         4.01        20.91        10.26        15.22 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 
       12.36        11.31        24.72        14.66        11.31        22.29 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-8099 TCGA-HF-7132 TCGA-HU-8238 
       15.65         0.62        19.53        17.06        77.29         1.51 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H0 
       18.15        28.96        24.30        22.75        25.81         2.10 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 
       23.80        33.40         6.51        10.62        11.70         5.56 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
       14.04        45.67        18.21        57.44         8.94        35.61 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PK 
        5.46        13.25        18.48        43.36        21.73        17.85 
TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F 
       39.45         9.50        11.24        43.66        38.93        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       16.14        27.55        12.43 

$`5P GAIN WILD-TYPE`
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 
       79.07        16.24         9.86        27.35        26.93        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7723 
       44.94        21.90        36.16        35.84        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        9.07        29.56        33.21        37.25        14.43        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        9.60        32.25         0.56        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 
        6.18        31.10        13.08        22.19         0.95         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72         5.39        25.18         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58         9.86        20.88        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51         0.46        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       13.35        11.21        12.10        12.53         7.17        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
       12.43        12.30        11.31        12.43         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
        1.02         8.05         4.01        29.98        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        9.01        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
      105.07        28.96        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85        13.35        17.19        15.98        12.79 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       12.33        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 
       14.76        26.43        11.24        11.44        20.32         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       21.27        11.38         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
        5.03        13.58         0.56         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       52.21        30.51        26.47         5.92        24.39        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.82        21.07         0.76         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        0.10         6.51         6.58        20.25         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       29.00        23.84        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1V TCGA-IN-AB1X 
       19.53         6.44         6.74        12.59        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53        63.62        37.64        36.95         3.72        19.73 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
      115.69       116.38        71.38        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        0.92        48.79        13.02        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71        42.64        60.85         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
       21.04         2.66        42.54        18.41        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        17.26         0.79 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.23              0.00 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            77.29            122.30 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            15.22             14.45 
[1] "0.2 - 77.3 (15.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         0        1       11        9         9        12
  5P GAIN WILD-TYPE       2       15       30       23        31        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED           0         17         13         10       12
  5P GAIN WILD-TYPE         3         64         50         29       32
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                15
  STAGE IB                11                30
  STAGE II                 9                23
  STAGE IIA                9                31
  STAGE IIB               12                44
  STAGE III                0                 3
  STAGE IIIA              17                64
  STAGE IIIB              13                50
  STAGE IIIC              10                29
  STAGE IV                12                32
[1] 11  2
[1] 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     1  25  50  21
  5P GAIN WILD-TYPE  22  68 146  98
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                22
  T2              25                68
  T3              50               146
  T4              21                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P GAIN MUTATED    26  26  22  21
  5P GAIN WILD-TYPE 104  93  64  67
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              26               104
  N1              26                93
  N2              22                64
  N3              21                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    87   8
  5P GAIN WILD-TYPE 302  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     87    8
  5P GAIN WILD-TYPE  302   22
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              87               302
  1               8                22
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    35  65
  5P GAIN WILD-TYPE 123 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     35   65
  5P GAIN WILD-TYPE  123  218
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              35               123
  MALE                65               218
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    71  17
  5P GAIN WILD-TYPE 251  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     71   17
  5P GAIN WILD-TYPE  251   59
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               71               251
  YES              17                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  5P GAIN MUTATED                                          3
  5P GAIN WILD-TYPE                                       10
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  5P GAIN MUTATED                                       7
  5P GAIN WILD-TYPE                                    65
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                       33
  5P GAIN WILD-TYPE                                                    130
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  5P GAIN MUTATED                                                   7
  5P GAIN WILD-TYPE                                                14
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                                  28
  5P GAIN WILD-TYPE                                                                54
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  5P GAIN MUTATED                                                    3
  5P GAIN WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  5P GAIN MUTATED                                                 17
  5P GAIN WILD-TYPE                                               62
D9V9, multiclass
                                                                   clus
vv                                                                  5P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         33
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              28
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               17
                                                                   clus
vv                                                                  5P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                54
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 62
[1] 7 2
[1] TRUE
[1] "dimension of 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    80   4   5   5
  5P GAIN WILD-TYPE 269  14  14  20
D9V10, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              80               269
  R1               4                14
  R2               5                14
  RX               5                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"
D9V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5P GAIN MUTATED      17                         2
  5P GAIN WILD-TYPE    71                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           0    63
  5P GAIN WILD-TYPE                                         1   215
D9V12, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                                  17                71
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  63               215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1  66
  5P GAIN WILD-TYPE   4 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   66
  5P GAIN WILD-TYPE    4  250
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              66               250
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    26  14
  5Q GAIN WILD-TYPE 220 155
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               40               375 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               14               155 
$`5Q GAIN MUTATED`
TCGA-KB-A93G TCGA-BR-7715 TCGA-BR-8284 TCGA-BR-8296 TCGA-BR-8365 TCGA-BR-8367 
       20.15        33.63         8.05        15.58        17.52        26.33 
TCGA-BR-A4PD TCGA-CD-8524 TCGA-CD-A486 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4455 
       20.65        12.76         6.31         7.99        54.08        12.03 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-6528 TCGA-D7-8576 
       18.97        12.00        15.02         4.01        15.22        14.66 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-8099 TCGA-HF-7132 TCGA-HU-8238 
       15.65         0.62        19.53        17.06        77.29         1.51 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-IN-A7NR TCGA-IN-A7NT 
       18.15        28.96         2.10        23.80         6.51        10.62 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-VQ-A8E0 TCGA-VQ-A91X 
       11.70         5.56        57.44        35.61        18.48         9.50 
TCGA-VQ-A94T TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6K 
       11.24        54.12        16.14        12.43 

$`5Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        9.86        27.35        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        32.25         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       22.19         0.95         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        1.02         8.05         4.01        14.01        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       11.24        11.31        11.44        20.32        22.29         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       21.27        11.38         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
        5.03        13.58         0.56         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       52.21        30.51        26.47         5.92        24.39        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
       20.25         0.26        12.95        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
        6.74        12.59        15.75        13.51         2.53        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       115.69       116.38        71.38         8.94        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y 
       20.81        32.88         1.71        42.64        60.85         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 
        5.72        66.81        21.04         2.66        42.54        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        17.13        26.04 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        17.26         0.79 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.62              0.00 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            77.29            122.30 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            15.40             14.47 
[1] "0.6 - 77.3 (15.4)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         0        0        7        4         6         4
  5Q GAIN WILD-TYPE       2       16       34       28        34        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           0          4          7          4        5
  5Q GAIN WILD-TYPE         3         77         56         35       39
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                16
  STAGE IB                 7                34
  STAGE II                 4                28
  STAGE IIA                6                34
  STAGE IIB                4                52
  STAGE III                0                 3
  STAGE IIIA               4                77
  STAGE IIIB               7                56
  STAGE IIIC               4                35
  STAGE IV                 5                39
[1] 11  2
[1] 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     0  12  23   8
  5Q GAIN WILD-TYPE  23  81 173 111
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                23
  T2              12                81
  T3              23               173
  T4               8               111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q GAIN MUTATED    15   9   9   9
  5Q GAIN WILD-TYPE 115 110  77  79
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              15               115
  N1               9               110
  N2               9                77
  N3               9                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    38   3
  5Q GAIN WILD-TYPE 351  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     38    3
  5Q GAIN WILD-TYPE  351   27
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              38               351
  1               3                27
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    13  30
  5Q GAIN WILD-TYPE 145 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     13   30
  5Q GAIN WILD-TYPE  145  253
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              13               145
  MALE                30               253
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    31   8
  5Q GAIN WILD-TYPE 291  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     31    8
  5Q GAIN WILD-TYPE  291   68
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               31               291
  YES               8                68
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  5Q GAIN MUTATED                                          2
  5Q GAIN WILD-TYPE                                       11
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  5Q GAIN MUTATED                                       3
  5Q GAIN WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                       13
  5Q GAIN WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  5Q GAIN MUTATED                                                   4
  5Q GAIN WILD-TYPE                                                17
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                                  12
  5Q GAIN WILD-TYPE                                                                70
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  5Q GAIN MUTATED                                                    2
  5Q GAIN WILD-TYPE                                                  6
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  5Q GAIN MUTATED                                                  6
  5Q GAIN WILD-TYPE                                               73
D10V9, multiclass
                                                                   clus
vv                                                                  5Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                6
                                                                   clus
vv                                                                  5Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 73
[1] 7 2
[1] TRUE
[1] "dimension of 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    37   1   2   1
  5Q GAIN WILD-TYPE 312  17  17  24
D10V10, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              37               312
  R1               1                17
  R2               2                17
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5Q GAIN MUTATED       8                         1
  5Q GAIN WILD-TYPE    80                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    24
  5Q GAIN WILD-TYPE                                         1   254
D10V12, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                                   8                80
  BLACK OR AFRICAN AMERICAN                               1                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  24               254
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  27
  5Q GAIN WILD-TYPE   5 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   27
  5Q GAIN WILD-TYPE    5  289
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              27               289
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    38  35
  6P GAIN WILD-TYPE 208 134
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               73               342 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               35               134 
$`6P GAIN MUTATED`
TCGA-CG-4460 TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4255 
       21.99        58.03        11.01         6.61         6.97         4.08 
TCGA-BR-4257 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
        9.67         9.17         9.21        35.24        33.63        18.15 
TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 
       11.44        29.42         2.66        14.04        14.79        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4PE 
        9.21        20.22        24.79        20.88        10.68        20.42 
TCGA-CD-5799 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4438 
       13.02         6.31        12.30        11.61         7.99        54.08 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       12.03        18.97        30.97        17.19        10.26        15.22 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A6EV 
       12.36        11.31        12.33        14.66        14.27        11.24 
TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8249 
       22.29         7.99         3.48         0.56         5.52        28.96 
TCGA-HU-A4GF TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RS 
       25.81        23.84        21.17         3.39        18.38        12.59 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW 
       14.04        45.67        18.21         8.61       122.30        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PE 
      115.69         8.94        13.25        13.02        18.48        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
        2.70        17.85        18.74         1.71         9.50         9.73 
TCGA-VQ-A94O 
       21.04 

$`6P GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.86        27.35        26.93        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         9.44         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       36.16        35.84        39.78        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       29.59         9.60        32.25         8.05         0.56        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        5.39         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.43        11.31        12.43         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
        8.05         4.01        14.01        29.98        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01         7.07        12.00         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 
       18.54        18.61        17.85        13.35        15.98        12.79 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.31        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         0.62        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       59.54         5.03        13.58         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       18.15        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        5.13        16.67        40.64       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       12.79         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        61.22        20.81        32.88        42.64        60.85 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        66.81         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.56              0.00 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           122.30            116.38 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           14.040            15.615 
[1] "0.6 - 122.3 (14.0)" "0.0 - 116.4 (15.6)"
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         1        3       12        6         5        10
  6P GAIN WILD-TYPE       1       13       29       26        35        46
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           0         17         10          4       10
  6P GAIN WILD-TYPE         3         64         53         35       34
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 3                13
  STAGE IB                12                29
  STAGE II                 6                26
  STAGE IIA                5                35
  STAGE IIB               10                46
  STAGE III                0                 3
  STAGE IIIA              17                64
  STAGE IIIB              10                53
  STAGE IIIC               4                35
  STAGE IV                10                34
[1] 11  2
[1] 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     4  24  33  17
  6P GAIN WILD-TYPE  19  69 163 102
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               4                19
  T2              24                69
  T3              33               163
  T4              17               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P GAIN MUTATED    24  20  19  15
  6P GAIN WILD-TYPE 106  99  67  73
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              24               106
  N1              20                99
  N2              19                67
  N3              15                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    69   5
  6P GAIN WILD-TYPE 320  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     69    5
  6P GAIN WILD-TYPE  320   25
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              69               320
  1               5                25
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    30  51
  6P GAIN WILD-TYPE 128 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     30   51
  6P GAIN WILD-TYPE  128  232
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              30               128
  MALE                51               232
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    63  12
  6P GAIN WILD-TYPE 259  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     63   12
  6P GAIN WILD-TYPE  259   64
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               63               259
  YES              12                64
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  6P GAIN MUTATED                                          2
  6P GAIN WILD-TYPE                                       11
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  6P GAIN MUTATED                                       3
  6P GAIN WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                       34
  6P GAIN WILD-TYPE                                                    129
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  6P GAIN MUTATED                                                   1
  6P GAIN WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                                  23
  6P GAIN WILD-TYPE                                                                59
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  6P GAIN MUTATED                                                    1
  6P GAIN WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  6P GAIN MUTATED                                                 17
  6P GAIN WILD-TYPE                                               62
D11V9, multiclass
                                                                   clus
vv                                                                  6P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         34
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              23
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               17
                                                                   clus
vv                                                                  6P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          129
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                59
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 62
[1] 7 2
[1] TRUE
[1] "dimension of 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    57   3   5   7
  6P GAIN WILD-TYPE 292  15  14  18
D11V10, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              57               292
  R1               3                15
  R2               5                14
  RX               7                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"
D11V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6P GAIN MUTATED      11                         4
  6P GAIN WILD-TYPE    77                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           1    55
  6P GAIN WILD-TYPE                                         0   223
D11V12, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               4                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  55               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2  60
  6P GAIN WILD-TYPE   3 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2   60
  6P GAIN WILD-TYPE    3  256
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              60               256
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    29  31
  6Q GAIN WILD-TYPE 217 138
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               60               355 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               31               138 
$`6Q GAIN MUTATED`
TCGA-CG-4460 TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4255 
       21.99        58.03        11.01         6.61         6.97         4.08 
TCGA-BR-4257 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8060 
        9.67         9.21        35.24        33.63        18.15        11.44 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 
       29.42         2.66        14.04        14.79        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4J1 TCGA-CD-5799 
       20.22        24.79        20.88        10.68         0.72        13.02 
TCGA-CD-A486 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4466 TCGA-CG-4477 TCGA-D7-6527 
        6.31         7.99        54.08        18.97        30.97        10.26 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6EV 
       15.22        12.36        11.31        12.33        14.27        11.24 
TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-A4BF TCGA-HU-A4GT TCGA-HU-A4H6 TCGA-IN-7808 
        7.99         3.48         5.52         6.51        21.17         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RS TCGA-MX-A666 TCGA-R5-A7O7 TCGA-RD-A7BT 
        3.39        18.38        12.59        14.04        45.67         8.61 
TCGA-RD-A8N6 TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
        8.94        13.25        13.02        18.48        22.19         2.70 
TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A94R 
       17.85        18.74        32.88         1.71         9.50        42.54 

$`6Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.86        27.35        26.93        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         9.44         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       21.90        36.16        35.84        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72         5.39         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        9.86         8.22        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82        12.43        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         1.02         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       29.98        19.07        12.03         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 
       17.85        13.35        17.19        15.98        12.79        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM 
       17.06        59.54         5.03        13.58         0.56         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL 
       15.68        33.40        36.36        18.81        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.44         6.74         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       15.75        13.51         2.53         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       36.95         3.72        19.73        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79         5.46        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        12.79         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W 
       11.70        21.83        61.22        20.81        42.64        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T 
        6.58         5.72        66.81        21.04         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.72              0.00 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            58.03            122.30 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           12.805            15.680 
[1] "0.7 - 58.0 (12.8)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1.6"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         1        3       10        5         4         6
  6Q GAIN WILD-TYPE       1       13       31       27        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           0         14          7          2       10
  6Q GAIN WILD-TYPE         3         67         56         37       34
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 3                13
  STAGE IB                10                31
  STAGE II                 5                27
  STAGE IIA                4                36
  STAGE IIB                6                50
  STAGE III                0                 3
  STAGE IIIA              14                67
  STAGE IIIB               7                56
  STAGE IIIC               2                37
  STAGE IV                10                34
[1] 11  2
[1] 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     4  20  23  17
  6Q GAIN WILD-TYPE  19  73 173 102
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               4                19
  T2              20                73
  T3              23               173
  T4              17               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q GAIN MUTATED    20  18  12  13
  6Q GAIN WILD-TYPE 110 101  74  75
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              20               110
  N1              18               101
  N2              12                74
  N3              13                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    54   6
  6Q GAIN WILD-TYPE 335  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     54    6
  6Q GAIN WILD-TYPE  335   24
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              54               335
  1               6                24
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    24  42
  6Q GAIN WILD-TYPE 134 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     24   42
  6Q GAIN WILD-TYPE  134  241
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              24               134
  MALE                42               241
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    51  11
  6Q GAIN WILD-TYPE 271  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     51   11
  6Q GAIN WILD-TYPE  271   65
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               51               271
  YES              11                65
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  6Q GAIN MUTATED                                          2
  6Q GAIN WILD-TYPE                                       11
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  6Q GAIN MUTATED                                       2
  6Q GAIN WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                       30
  6Q GAIN WILD-TYPE                                                    133
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  6Q GAIN MUTATED                                                   0
  6Q GAIN WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                                  19
  6Q GAIN WILD-TYPE                                                                63
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  6Q GAIN MUTATED                                                    1
  6Q GAIN WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  6Q GAIN MUTATED                                                 12
  6Q GAIN WILD-TYPE                                               67
D12V9, multiclass
                                                                   clus
vv                                                                  6Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         30
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              19
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               12
                                                                   clus
vv                                                                  6Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 67
[1] 7 2
[1] TRUE
[1] "dimension of 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    46   2   4   6
  6Q GAIN WILD-TYPE 303  16  15  19
D12V10, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              46               303
  R1               2                16
  R2               4                15
  RX               6                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"
D12V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6Q GAIN MUTATED       8                         4
  6Q GAIN WILD-TYPE    80                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           1    44
  6Q GAIN WILD-TYPE                                         0   234
D12V12, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                                   8                80
  BLACK OR AFRICAN AMERICAN                               4                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  44               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  46
  6Q GAIN WILD-TYPE   3 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   46
  6Q GAIN WILD-TYPE    3  270
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              46               270
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   111  77
  7P GAIN WILD-TYPE 135  92
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              188               227 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               77                92 
$`7P GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        22.98        79.07         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 
       27.35        26.93        11.70        11.01         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
        4.64         9.67        17.29         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
       18.05        40.21         9.21        35.24        33.63        18.15 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8284 
        3.45        29.56        33.21        14.43         0.69         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 
        0.56        29.42         2.20        15.58         7.40        13.08 
TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8486 
        0.95         3.32        14.79         7.36         5.39        20.22 
TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
        1.12        32.58         9.86         8.22        10.68        13.87 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 
       34.98         1.48         0.72         0.53        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 
       20.65        20.42         1.15        21.44        13.02        13.18 
TCGA-CD-5804 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.10        12.33        12.39        15.39        12.07        12.43 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 
        6.31        12.43        11.61         6.58        12.20        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4469 
       27.02        15.95         7.99         4.01        14.01         7.07 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5733 TCGA-CG-5734 
       12.00        36.00        12.03        28.96        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 
       12.66        20.91        19.13        18.84        18.54        17.19 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       15.22        15.98        12.36        12.33        24.72        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       17.19        18.21        14.66        21.14        20.91        16.44 
TCGA-D7-A4YX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
       36.43        22.29        15.65        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-A9TM TCGA-HF-7134 
       19.53        14.07        22.29        17.06         6.21        52.21 
TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD 
       26.47        28.96        24.30        24.26         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
       25.81         8.98         0.10        20.25         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 
       29.00        23.84        23.80        21.17        33.40         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RS 
       18.81         3.39        18.38        13.35         6.44        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 
        6.51        11.70         5.56        63.62        37.64        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV 
       18.21         8.52        74.53         6.08         8.61       122.30 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
       57.44         8.94        48.79        13.25        13.02        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PH 
       21.73        37.41        34.29        46.26         2.50        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       17.85        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        20.81         1.71        42.64        60.85         9.50 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 
        2.01         4.54        21.04        42.54        11.24        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       38.93        32.94        54.12        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

$`7P GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK 
       47.05        16.24        58.03        26.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        9.44         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6707 
       13.87        13.68        19.33        39.12        26.10        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       36.16        35.84        39.78        15.32        28.73         9.07 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 
       37.25        11.44        29.59         9.60        32.25         2.66 
TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       19.96         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 
       26.33         4.31        14.04        11.80        31.27        25.05 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        25.18         9.21        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       20.88        34.13         7.53         6.08        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
       12.89         8.98        14.17        28.34         0.66         0.46 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
       16.14         5.13        13.41        13.15        13.35        11.21 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 
       12.76        12.59        12.53         7.17        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.64        12.82        12.30        11.31        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 
        3.02         1.02         8.05        54.08        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01        18.97        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 
       65.10         4.01        69.04        25.71        20.55        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8572 
       17.85        13.35        10.26        12.79        11.31        16.80 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27         5.92        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.31        11.44        20.32         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-8209 
        7.13         0.62         7.99        21.27        11.38        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         0.56         5.52        77.29        63.06 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        18.15        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       22.82        21.07         0.76         5.59        22.68        24.20 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       11.77        21.37        29.98         6.51         6.58         0.26 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       14.07        15.68        36.36        12.46        19.53         6.74 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A5UG 
       10.62        15.75        13.51         2.53        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       19.73        14.04         4.60         9.24        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       35.61        16.87        19.04         5.79         0.92         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PD 
       18.48        38.14        37.22         7.73        30.97        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       22.19         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91Y 
       13.35        29.59        64.57        61.22        32.88         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       55.56         9.04        55.43         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
        2.66        18.41        28.41        17.13        26.04 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              0.1               0.0 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           122.30            116.38 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            15.80             14.04 
[1] "0.1 - 122.3 (15.8)" "0.0 - 116.4 (14.0)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         2        7       19       13        17        23
  7P GAIN WILD-TYPE       0        9       22       19        23        33
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           2         37         31         22       17
  7P GAIN WILD-TYPE         1         44         32         17       27
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  2                 0
  STAGE IA                 7                 9
  STAGE IB                19                22
  STAGE II                13                19
  STAGE IIA               17                23
  STAGE IIB               23                33
  STAGE III                2                 1
  STAGE IIIA              37                44
  STAGE IIIB              31                32
  STAGE IIIC              22                17
  STAGE IV                17                27
[1] 11  2
[1] 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    11  38  94  53
  7P GAIN WILD-TYPE  12  55 102  66
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              11                12
  T2              38                55
  T3              94               102
  T4              53                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7P GAIN MUTATED   60 48 41 45
  7P GAIN WILD-TYPE 70 71 45 43
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              60                70
  N1              48                71
  N2              41                45
  N3              45                43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   180  11
  7P GAIN WILD-TYPE 209  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    180   11
  7P GAIN WILD-TYPE  209   19
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             180               209
  1              11                19
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    64 138
  7P GAIN WILD-TYPE  94 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     64  138
  7P GAIN WILD-TYPE   94  145
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              64                94
  MALE               138               145
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   147  34
  7P GAIN WILD-TYPE 175  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    147   34
  7P GAIN WILD-TYPE  175   42
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              147               175
  YES              34                42
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  7P GAIN MUTATED                                          8
  7P GAIN WILD-TYPE                                        5
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  7P GAIN MUTATED                                      23
  7P GAIN WILD-TYPE                                    49
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                       74
  7P GAIN WILD-TYPE                                                     89
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  7P GAIN MUTATED                                                   7
  7P GAIN WILD-TYPE                                                14
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                                  45
  7P GAIN WILD-TYPE                                                                37
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  7P GAIN MUTATED                                                    3
  7P GAIN WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  7P GAIN MUTATED                                                 40
  7P GAIN WILD-TYPE                                               39
D13V9, multiclass
                                                                   clus
vv                                                                  7P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          23
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         74
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              45
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               40
                                                                   clus
vv                                                                  7P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            49
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           89
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 39
[1] 7 2
[1] TRUE
[1] "dimension of 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   165   7   7  10
  7P GAIN WILD-TYPE 184  11  12  15
D13V10, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             165               184
  R1               7                11
  R2               7                12
  RX              10                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"
D13V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED      39                         8
  7P GAIN WILD-TYPE    49                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           1   125
  7P GAIN WILD-TYPE                                         0   153
D13V12, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                                  39                49
  BLACK OR AFRICAN AMERICAN                               8                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 125               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"
D13V13, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     3 138
  7P GAIN WILD-TYPE   2 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3  138
  7P GAIN WILD-TYPE    2  178
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO             138               178
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    94  63
  7Q GAIN WILD-TYPE 152 106
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              157               258 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               63               106 
$`7Q GAIN MUTATED`
TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       22.98        79.07         0.23        20.15         9.86        27.35 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
       11.70        11.01         6.61         6.97         4.64        18.35 
TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        9.67        17.29         9.17        32.78        25.61        18.05 
TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7958 
       40.21         9.21        35.24        33.63        18.15        29.56 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 
       33.21        14.43         8.05         0.56        29.42         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 
       15.58         7.40        13.08         0.95         3.32        14.79 
TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 
        7.36         5.39        20.22         1.12        32.58         9.86 
TCGA-BR-8690 TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 
       10.68        12.89         0.72         0.53        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 
       20.65        20.42         1.15        13.02        13.18        12.10 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG 
       12.39        15.39        12.07        12.43        12.43         6.58 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4440 
       12.20        20.02        27.02        15.95         7.99         4.01 
TCGA-CG-4441 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 
       14.01         7.07        12.00        36.00        12.03        28.96 
TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       21.07        12.66        20.91        19.13        18.84        18.54 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 
       17.19        10.26        15.22        24.72        19.50        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-D7-A6F2 
       14.66        21.14        20.91        16.44        22.29        15.65 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       14.47        72.23         3.48        14.07        22.29        17.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF 
       52.21        26.47        28.96        24.30        24.26        25.81 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        8.98         0.10        20.25         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NR 
       23.84        18.81         3.39        13.35         6.44         6.51 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       11.70         5.56        63.62        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 
       74.53         6.08         8.61       122.30        57.44         8.94 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79        13.25        13.02        43.36        21.73        37.41 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       34.29        46.26         2.50        17.85        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       39.45        11.70        21.83        20.81         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94T 
       60.85         9.50         2.01         4.54        21.04        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-ZA-A8F6 
       43.66        38.93        32.94        54.12        16.14        17.26 
TCGA-ZQ-A9CR 
        0.79 

$`7Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-EQ-A4SO TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 
       47.05        21.99        16.24        26.93        58.03        26.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
       19.56         9.47         9.44         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        13.68        19.33        39.12        26.10 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       21.90        36.16        35.84        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        3.45         9.07        37.25        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 
        9.60        32.25         2.66        19.96         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19        17.52        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       11.80        31.27        25.05         3.72        25.18         9.21 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
       26.73        24.79        31.96        20.88         8.22        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
       28.57         8.98        14.17        28.34         0.66         0.46 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 
       21.44        16.14         5.13        13.41        13.15        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       11.21        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       12.30        12.59        11.64        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 
       11.31        11.61        11.77        12.62         3.02         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        8.05        54.08        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        9.01        18.97        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 
       69.04         7.99        25.71        20.55        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       13.35        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       16.80        18.21        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       21.27        11.38        19.53        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
        0.56         5.52         6.21        77.29        63.06        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       21.07         0.76         5.59        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU 
       22.75        11.77        21.37        29.98         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        0.26        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       36.36         3.45        18.38        12.46        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H 
       12.59        10.62        15.75        13.51         2.53        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A804 TCGA-R5-A805 
       36.95         3.72        19.73        14.04         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         5.13        16.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
      116.38        71.38        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
        0.92         5.46        18.48        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       30.97        16.31        22.19        12.79         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       61.22        18.74        32.88         9.73        55.56         9.04 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        66.81         2.66        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       18.41        28.41        17.13        26.04        27.55        12.43 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.1               0.0 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           122.30            116.38 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           15.650            14.055 
[1] "0.1 - 122.3 (15.7)" "0.0 - 116.4 (14.1)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         1        6       17       14        14        16
  7Q GAIN WILD-TYPE       1       10       24       18        26        40
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           2         30         26         19       15
  7Q GAIN WILD-TYPE         1         51         37         20       29
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 6                10
  STAGE IB                17                24
  STAGE II                14                18
  STAGE IIA               14                26
  STAGE IIB               16                40
  STAGE III                2                 1
  STAGE IIIA              30                51
  STAGE IIIB              26                37
  STAGE IIIC              19                20
  STAGE IV                15                29
[1] 11  2
[1] 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     8  35  79  42
  7Q GAIN WILD-TYPE  15  58 117  77
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               8                15
  T2              35                58
  T3              79               117
  T4              42                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7Q GAIN MUTATED   52 39 33 38
  7Q GAIN WILD-TYPE 78 80 53 50
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              52                78
  N1              39                80
  N2              33                53
  N3              38                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   150   9
  7Q GAIN WILD-TYPE 239  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    150    9
  7Q GAIN WILD-TYPE  239   21
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             150               239
  1               9                21
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    54 117
  7Q GAIN WILD-TYPE 104 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     54  117
  7Q GAIN WILD-TYPE  104  166
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              54               104
  MALE               117               166
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   125  27
  7Q GAIN WILD-TYPE 197  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    125   27
  7Q GAIN WILD-TYPE  197   49
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              125               197
  YES              27                49
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  7Q GAIN MUTATED                                          6
  7Q GAIN WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  7Q GAIN MUTATED                                      20
  7Q GAIN WILD-TYPE                                    52
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                       63
  7Q GAIN WILD-TYPE                                                    100
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  7Q GAIN MUTATED                                                   6
  7Q GAIN WILD-TYPE                                                15
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                                  40
  7Q GAIN WILD-TYPE                                                                42
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  7Q GAIN MUTATED                                                    3
  7Q GAIN WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  7Q GAIN MUTATED                                                 31
  7Q GAIN WILD-TYPE                                               48
D14V9, multiclass
                                                                   clus
vv                                                                  7Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          20
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         63
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               31
                                                                   clus
vv                                                                  7Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            52
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          100
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                42
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 48
[1] 7 2
[1] TRUE
[1] "dimension of 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   139   4   6  12
  7Q GAIN WILD-TYPE 210  14  13  13
D14V10, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             139               210
  R1               4                14
  R2               6                13
  RX              12                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"
D14V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED      31                         7
  7Q GAIN WILD-TYPE    57                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           1   106
  7Q GAIN WILD-TYPE                                         0   172
D14V12, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                                  31                57
  BLACK OR AFRICAN AMERICAN                               7                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 106               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"
D14V13, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     3 116
  7Q GAIN WILD-TYPE   2 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3  116
  7Q GAIN WILD-TYPE    2  200
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO             116               200
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   104  67
  8P GAIN WILD-TYPE 142 102
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              171               244 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               67               102 
$`8P GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
       27.35        26.93        26.70        11.01         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        6.97         4.64        30.90         4.08         9.34         9.67 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6707 
       34.68        15.95        13.87        17.29        13.68        19.89 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       30.90        31.20        44.94        35.24        35.84        33.63 
TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8297 
        9.07        11.44        29.59         9.60         8.05         7.40 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31        14.04         3.32        31.27         7.36        25.05 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 
        5.39         9.21        20.22         9.34        28.14         7.53 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J5 TCGA-BR-A4J7 
        7.53        34.98         1.48        27.55        28.34        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8530 
        0.46        20.42        16.14        13.15        11.21        12.39 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 
       12.43         6.31        12.30         6.58        12.62        20.02 
TCGA-CG-4305 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       15.95        14.01        12.03         0.00        18.97         7.07 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
       12.00        36.00         0.99        15.02        28.96        65.10 
TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6526 
       21.07        20.91        19.13        18.84        17.85        17.19 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV 
       12.79        12.36        12.33        14.66        20.91         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       36.43        14.76        11.24        11.31        11.44        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-A4BF 
        8.38         4.34         0.62        21.27        19.53         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 
        6.21        77.29        52.21        30.51        26.47        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       18.15        22.32        24.30        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        29.98         8.98         0.10 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        0.26         2.10        29.00        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NR 
       15.68         3.45         3.39        13.35        12.59         6.51 
TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       10.62        63.62        37.64        19.73         8.52        74.53 
TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
        6.08        16.67       115.69        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P2 
        5.79         0.92        48.79         5.46        13.02        38.14 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH 
        7.73        30.97        34.29        16.31        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91A 
        2.70         9.27        23.41        29.59        64.57        39.45 
TCGA-VQ-A91E TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
       21.83        42.64        60.85         6.58         5.72        21.04 
TCGA-VQ-A94R TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       42.54        17.26         0.79 

$`8P GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN 
       47.05        22.98        58.03        11.70        19.56         9.44 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35         4.08         6.18         9.57         6.61 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7197 
       18.05        12.16         8.98        40.21        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       36.16        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8081 
       29.56        33.21        37.25        14.43         0.69        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 
        0.95        26.33        11.80        14.79         3.72        25.18 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 
        1.12        12.79        27.12         6.28        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.13        13.87         6.08        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.72        14.17         0.53         0.66        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
        1.15        21.44         5.13        13.41        13.02        13.18 
TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.35        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.82        11.31        12.43        11.61        12.20        11.77 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 
        4.01        29.98        19.07         9.01        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5730 
        1.02         0.99         6.02       105.07        12.03         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 
       69.04         7.99        25.71        12.66        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
       18.61        13.35        10.26        15.22        15.98        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.27        16.44        13.78        26.43        20.32        15.65 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
       19.96         7.13         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 
       13.58         0.56        63.06         1.51         5.92        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.82        21.07         0.76         5.59        11.77        21.37 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HD 
        6.51         6.58        20.25        12.95        21.17        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       36.36        18.81        18.38        12.46        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.74        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A804 
       36.95         3.72        14.04        45.67        18.21         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DV 
       40.64       116.38        71.38        57.44         8.94        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PC 
       18.48        43.36        21.73        37.41        37.22        46.26 
TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PY 
        2.50        17.85         1.87        15.65        13.35        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       73.41        11.70        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        1.71         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
       55.43         4.54        66.81         2.66        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       26.04        16.14        27.55        12.43 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.00              0.26 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           115.69            122.30 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            16.14             14.22 
[1] "0.0 - 115.7 (16.1)" "0.3 - 122.3 (14.2)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         0        8       20       13        17        28
  8P GAIN WILD-TYPE       2        8       21       19        23        28
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           1         31         19         17       16
  8P GAIN WILD-TYPE         2         50         44         22       28
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 8                 8
  STAGE IB                20                21
  STAGE II                13                19
  STAGE IIA               17                23
  STAGE IIB               28                28
  STAGE III                1                 2
  STAGE IIIA              31                50
  STAGE IIIB              19                44
  STAGE IIIC              17                22
  STAGE IV                16                28
[1] 11  2
[1] 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    12  43  72  49
  8P GAIN WILD-TYPE  11  50 124  70
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              12                11
  T2              43                50
  T3              72               124
  T4              49                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8P GAIN MUTATED   56 46 30 39
  8P GAIN WILD-TYPE 74 73 56 49
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              56                74
  N1              46                73
  N2              30                56
  N3              39                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   163  12
  8P GAIN WILD-TYPE 226  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    163   12
  8P GAIN WILD-TYPE  226   18
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             163               226
  1              12                18
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    79 104
  8P GAIN WILD-TYPE  79 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     79  104
  8P GAIN WILD-TYPE   79  179
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              79                79
  MALE               104               179
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   135  30
  8P GAIN WILD-TYPE 187  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    135   30
  8P GAIN WILD-TYPE  187   46
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              135               187
  YES              30                46
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  8P GAIN MUTATED                                          7
  8P GAIN WILD-TYPE                                        6
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  8P GAIN MUTATED                                      31
  8P GAIN WILD-TYPE                                    41
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                       62
  8P GAIN WILD-TYPE                                                    101
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  8P GAIN MUTATED                                                  13
  8P GAIN WILD-TYPE                                                 8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                                  31
  8P GAIN WILD-TYPE                                                                51
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  8P GAIN MUTATED                                                    6
  8P GAIN WILD-TYPE                                                  2
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  8P GAIN MUTATED                                                 31
  8P GAIN WILD-TYPE                                               48
D15V9, multiclass
                                                                   clus
vv                                                                  8P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          31
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         62
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              31
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               31
                                                                   clus
vv                                                                  8P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            41
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          101
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                51
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 48
[1] 7 2
[1] TRUE
[1] "dimension of 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   140  11   6  15
  8P GAIN WILD-TYPE 209   7  13  10
D15V10, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0             140               209
  R1              11                 7
  R2               6                13
  RX              15                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"
D15V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8P GAIN MUTATED      34                         5
  8P GAIN WILD-TYPE    54                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           0   117
  8P GAIN WILD-TYPE                                         1   161
D15V12, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                                  34                54
  BLACK OR AFRICAN AMERICAN                               5                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 117               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"
D15V13, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2 131
  8P GAIN WILD-TYPE   3 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2  131
  8P GAIN WILD-TYPE    3  185
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             131               185
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   134  89
  8Q GAIN WILD-TYPE 112  80
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              223               192 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               89                80 
$`8Q GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK 
       27.35        26.93        58.03        26.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4255 
        9.44         6.61         6.97         4.64        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.34         9.67        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-6803 
       13.68         9.17        19.89        12.16        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       44.94         9.21        35.24        35.84        33.63        39.78 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        9.07        29.56        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8367 
        8.05        15.58         7.40         6.18        13.08        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31        14.04         3.32        31.27         7.36        25.05 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        5.39         9.21        20.22        12.79         9.34        28.14 
TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
        7.53        32.58         8.22        13.87         7.53        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
        1.48        27.55         0.72        28.34        32.52         0.46 
TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 
       16.14        13.15        11.21        12.59        12.53        12.39 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG 
       15.39        12.82        12.43         6.31        12.30         6.58 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
       12.62        20.02        15.95         8.05        54.08        14.01 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 
       12.03         0.00        18.97         7.07        12.00        36.00 
TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6524 
       21.07        12.66        20.91        19.13        18.84        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        17.19        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       12.33        14.66        20.91        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 
       14.76        11.24        11.31        11.44        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
        8.38         4.34         0.62         7.99        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        3.48        19.53         0.56         5.52         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         5.92        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       22.32         0.76        24.30        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.51         0.26         2.10        29.00        23.84        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL 
       14.07        15.68        33.40         3.45         3.39        13.35 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-KB-A6F7 
        6.44         6.74        12.59         6.51        10.62        63.62 
TCGA-KB-A93H TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       37.64        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N4 
       74.53         6.08        11.05        16.67       115.69        71.38 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
        5.46        13.25        13.02        38.14         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       34.29        16.31        22.19        12.79         2.70         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E 
       23.41        13.35        29.59        64.57        39.45        21.83 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
       42.64        60.85        55.56         6.58         5.72        21.04 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       42.54        18.41        43.66        16.14        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

$`8Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4191 
       47.05        22.98        11.70        19.56         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6458 TCGA-BR-6563 
        4.08         6.18         9.57         6.61        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 
       26.10        32.78        25.61        18.05         8.98        40.21 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       21.90        36.16        18.15        15.32        28.73         3.45 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
       33.21        37.25        14.43        32.25         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.66        19.96         2.20        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 
       17.52         0.95        11.80        14.79         3.72        25.18 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        1.12        27.12         6.28        26.73        24.79        31.96 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IV 
        9.86        20.88        10.68        34.13         6.08        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J8 
       12.89         8.98        14.17         0.53         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8527 
       13.02        13.18        13.35        12.10        12.76         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-A489 
       12.33        12.30        12.59        11.64        12.07        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4301 TCGA-CG-4304 
       12.43        11.61        12.20        11.77         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 
        1.02         7.99         4.01        29.98        19.07         9.01 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
       30.97         6.97         1.02         0.99         6.02       105.07 
TCGA-CG-5724 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
       12.03         7.99        25.71        20.55        18.54        18.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.26        15.22        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EZ 
       18.21        21.14        14.27        13.78        26.43        20.32 
TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 
       19.96         7.13        14.47        11.38        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7133 TCGA-HU-8238 
       17.06        59.54         5.03        13.58        63.06         1.51 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GJ 
       28.96        22.82        21.07         5.59        11.77        21.37 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 
        6.58        20.25        12.95        21.17        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       18.38        12.46        19.53        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-R5-A804 TCGA-R5-A805 
        2.53         5.56        36.95         3.72         4.60         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         5.13       122.30        37.91        40.64       116.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       57.44         8.94        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.22        46.26         2.50        17.85         1.87        15.65 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       14.33        73.41        11.70        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 
       32.88         1.71         9.50         9.73         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 
       55.43         4.54        66.81         2.66        11.24        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       38.93        32.94        17.13        54.12        26.04        27.55 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.00              0.26 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           115.69            122.30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            14.66             15.27 
[1] "0.0 - 115.7 (14.7)" "0.3 - 122.3 (15.3)"
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         1       11       23       16        20        36
  8Q GAIN WILD-TYPE       1        5       18       16        20        20
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           1         46         27         24       20
  8Q GAIN WILD-TYPE         2         35         36         15       24
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                11                 5
  STAGE IB                23                18
  STAGE II                16                16
  STAGE IIA               20                20
  STAGE IIB               36                20
  STAGE III                1                 2
  STAGE IIIA              46                35
  STAGE IIIB              27                36
  STAGE IIIC              24                15
  STAGE IV                20                24
[1] 11  2
[1] 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   16 54 99 63
  8Q GAIN WILD-TYPE  7 39 97 56
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              16                 7
  T2              54                39
  T3              99                97
  T4              63                56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8Q GAIN MUTATED   70 65 40 50
  8Q GAIN WILD-TYPE 60 54 46 38
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              70                60
  N1              65                54
  N2              40                46
  N3              50                38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   211  14
  8Q GAIN WILD-TYPE 178  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    211   14
  8Q GAIN WILD-TYPE  178   16
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             211               178
  1              14                16
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    95 145
  8Q GAIN WILD-TYPE  63 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     95  145
  8Q GAIN WILD-TYPE   63  138
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              95                63
  MALE               145               138
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   174  41
  8Q GAIN WILD-TYPE 148  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    174   41
  8Q GAIN WILD-TYPE  148   35
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              174               148
  YES              41                35
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  8Q GAIN MUTATED                                          8
  8Q GAIN WILD-TYPE                                        5
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  8Q GAIN MUTATED                                      34
  8Q GAIN WILD-TYPE                                    38
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                       86
  8Q GAIN WILD-TYPE                                                     77
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  8Q GAIN MUTATED                                                  15
  8Q GAIN WILD-TYPE                                                 6
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                                  45
  8Q GAIN WILD-TYPE                                                                37
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  8Q GAIN MUTATED                                                    6
  8Q GAIN WILD-TYPE                                                  2
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  8Q GAIN MUTATED                                                 44
  8Q GAIN WILD-TYPE                                               35
D16V9, multiclass
                                                                   clus
vv                                                                  8Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          34
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         86
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              45
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               44
                                                                   clus
vv                                                                  8Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            38
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           77
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 35
[1] 7 2
[1] TRUE
[1] "dimension of 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   184  15   7  17
  8Q GAIN WILD-TYPE 165   3  12   8
D16V10, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             184               165
  R1              15                 3
  R2               7                12
  RX              17                 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"
D16V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8Q GAIN MUTATED      45                         8
  8Q GAIN WILD-TYPE    43                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           0   155
  8Q GAIN WILD-TYPE                                         1   123
D16V12, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                                  45                43
  BLACK OR AFRICAN AMERICAN                               8                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 155               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"
D16V13, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     4 174
  8Q GAIN WILD-TYPE   1 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4  174
  8Q GAIN WILD-TYPE    1  142
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 1
  NOT HISPANIC OR LATINO             174               142
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    40  16
  9P GAIN WILD-TYPE 206 153
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               56               359 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               153 
$`9P GAIN MUTATED`
TCGA-CG-4444 TCGA-FP-A8CX TCGA-KB-A93G TCGA-B7-A5TK TCGA-BR-6456 TCGA-BR-6707 
       47.05         0.23        20.15         9.47        17.29        19.89 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8295 
       35.84        33.63        33.21         9.60         2.66         2.20 
TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5801 
       12.79        32.58         0.53         0.46        13.41        13.18 
TCGA-CD-8535 TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4477 TCGA-D7-6528 TCGA-D7-6818 
       12.82        12.20         7.99        30.97        15.22        12.36 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-EQ-5647 TCGA-F1-A448 
       12.33        18.21        14.76        11.44         0.62        21.27 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 
       77.29        52.21        30.51        28.96         0.76        24.26 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-8663 
       22.75         8.98         2.10        12.95        23.80         3.39 
TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-R5-A7ZI TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 
        6.44        63.62        74.53       122.30       115.69        35.61 
TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PP TCGA-VQ-A91S TCGA-VQ-A91Z TCGA-VQ-A922 
        5.46        46.26        23.41        32.88        55.56         9.04 
TCGA-VQ-A928 TCGA-VQ-AA6F 
        5.72        54.12 

$`9P GAIN WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU 
       21.99        22.98        79.07        16.24         9.86        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       26.93        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7716 
       44.94        21.90         9.21        36.16        35.24        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       37.25        14.43        11.44         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        29.42        19.96        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
       16.14         5.13        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        12.00         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.79        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       36.43        13.78        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         6.21        63.06        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        18.15        22.32        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       24.30         5.59        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
       20.25         0.26        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
       15.68        33.40        36.36         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         5.13        16.67        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        0.92        48.79        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       17.85         1.87         9.27        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        18.74        20.81         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.50         9.73         2.01        55.43         4.54         6.58 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        17.13        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.23              0.00 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           122.30            116.38 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           16.255            14.660 
[1] "0.2 - 122.3 (16.3)" "0.0 - 116.4 (14.7)"
[1] "hr=" "1.7"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         0        3        8        3         5         8
  9P GAIN WILD-TYPE       2       13       33       29        35        48
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           0         11          8          5        6
  9P GAIN WILD-TYPE         3         70         55         34       38
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                13
  STAGE IB                 8                33
  STAGE II                 3                29
  STAGE IIA                5                35
  STAGE IIB                8                48
  STAGE III                0                 3
  STAGE IIIA              11                70
  STAGE IIIB               8                55
  STAGE IIIC               5                34
  STAGE IV                 6                38
[1] 11  2
[1] 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  14  22  16
  9P GAIN WILD-TYPE  17  79 174 103
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               6                17
  T2              14                79
  T3              22               174
  T4              16               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P GAIN MUTATED    18  17  10  12
  9P GAIN WILD-TYPE 112 102  76  76
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              18               112
  N1              17               102
  N2              10                76
  N3              12                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    54   3
  9P GAIN WILD-TYPE 335  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     54    3
  9P GAIN WILD-TYPE  335   27
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              54               335
  1               3                27
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    20  39
  9P GAIN WILD-TYPE 138 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     20   39
  9P GAIN WILD-TYPE  138  244
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              20               138
  MALE                39               244
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    39  16
  9P GAIN WILD-TYPE 283  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     39   16
  9P GAIN WILD-TYPE  283   60
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               39               283
  YES              16                60
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  9P GAIN MUTATED                                          3
  9P GAIN WILD-TYPE                                       10
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  9P GAIN MUTATED                                       7
  9P GAIN WILD-TYPE                                    65
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                       17
  9P GAIN WILD-TYPE                                                    146
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  9P GAIN MUTATED                                                   8
  9P GAIN WILD-TYPE                                                13
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                                   8
  9P GAIN WILD-TYPE                                                                74
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  9P GAIN MUTATED                                                    3
  9P GAIN WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  9P GAIN MUTATED                                                 13
  9P GAIN WILD-TYPE                                               66
D17V9, multiclass
                                                                   clus
vv                                                                  9P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         17
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               13
                                                                   clus
vv                                                                  9P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                74
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 66
[1] 7 2
[1] TRUE
[1] "dimension of 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    49   3   1   2
  9P GAIN WILD-TYPE 300  15  18  23
D17V10, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              49               300
  R1               3                15
  R2               1                18
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9P GAIN MUTATED      15                         1
  9P GAIN WILD-TYPE    73                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           0    34
  9P GAIN WILD-TYPE                                         1   244
D17V12, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                                  15                73
  BLACK OR AFRICAN AMERICAN                               1                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  34               244
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  41
  9P GAIN WILD-TYPE   3 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   41
  9P GAIN WILD-TYPE    3  275
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              41               275
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    48  25
  9Q GAIN WILD-TYPE 198 144
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               73               342 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               25               144 
$`9Q GAIN MUTATED`
TCGA-CG-4444 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-B7-A5TK TCGA-BR-4191 
       47.05         0.23        20.15        27.35         9.47        18.35 
TCGA-BR-6456 TCGA-BR-6707 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       17.29        19.89        35.24        35.84        33.63        18.15 
TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8588 
       33.21         9.60         2.66         2.20         6.18        12.79 
TCGA-BR-8682 TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       32.58        34.98         0.53         0.46        20.65        20.42 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8535 TCGA-CG-4436 TCGA-CG-4477 
       13.41        13.18        12.10        12.82         7.99        30.97 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EY 
       17.19        15.22        12.36        14.27        14.76        11.44 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-7735 TCGA-HF-7132 
       15.65         8.38         0.62        21.27         3.48        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 
       52.21        30.51         1.51        28.96         0.76        24.26 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RP 
       22.75         8.98        23.80         3.45         3.39         6.44 
TCGA-KB-A6F7 TCGA-R5-A7ZI TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT 
       63.62        74.53       122.30       115.69        35.61        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PP TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V 
        5.46        46.26        23.41        18.74        32.88        42.64 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A94T TCGA-VQ-AA6F 
        9.50        55.56         9.04         5.72        11.24        54.12 
TCGA-VQ-AA6K 
       12.43 

$`9Q GAIN WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A94U 
       21.99        22.98        79.07        16.24         9.86        26.93 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 
       26.10         9.17        32.78        25.61        18.05        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
        9.21        36.16        39.78        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
       29.59        32.25         8.05         0.56        29.42        19.96 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 
        5.39        25.18         9.21        20.22         1.12        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52        13.51         1.15        21.44        16.14         5.13 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.02        13.15        13.35        11.21        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       13.35        10.26        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        36.43        13.78 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 
       26.43        11.24        11.31        20.32        22.29         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
       19.96         7.13         7.99        14.47        72.23        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 
       13.58         0.56         5.52         6.21        63.06        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        18.15        22.32        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       24.30         5.59        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       21.17        14.07        15.68        33.40        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        13.35        19.53         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       17.85         1.87         9.27        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 
       61.22        20.81         1.71        60.85         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         4.54         6.58        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.54        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        16.14        27.55        17.26         0.79 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.23              0.00 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           122.30            116.38 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            17.29             14.38 
[1] "0.2 - 122.3 (17.3)" "0.0 - 116.4 (14.4)"
[1] "hr=" "1.4"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         0        4       10        4         5        10
  9Q GAIN WILD-TYPE       2       12       31       28        35        46
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           0         15         10          5        8
  9Q GAIN WILD-TYPE         3         66         53         34       36
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 4                12
  STAGE IB                10                31
  STAGE II                 4                28
  STAGE IIA                5                35
  STAGE IIB               10                46
  STAGE III                0                 3
  STAGE IIIA              15                66
  STAGE IIIB              10                53
  STAGE IIIC               5                34
  STAGE IV                 8                36
[1] 11  2
[1] 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     7  17  30  21
  9Q GAIN WILD-TYPE  16  76 166  98
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               7                16
  T2              17                76
  T3              30               166
  T4              21                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q GAIN MUTATED    23  23  14  15
  9Q GAIN WILD-TYPE 107  96  72  73
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              23               107
  N1              23                96
  N2              14                72
  N3              15                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    70   4
  9Q GAIN WILD-TYPE 319  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     70    4
  9Q GAIN WILD-TYPE  319   26
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              70               319
  1               4                26
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    24  53
  9Q GAIN WILD-TYPE 134 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     24   53
  9Q GAIN WILD-TYPE  134  230
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              24               134
  MALE                53               230
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    53  20
  9Q GAIN WILD-TYPE 269  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     53   20
  9Q GAIN WILD-TYPE  269   56
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               53               269
  YES              20                56
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  9Q GAIN MUTATED                                          4
  9Q GAIN WILD-TYPE                                        9
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  9Q GAIN MUTATED                                       9
  9Q GAIN WILD-TYPE                                    63
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                       24
  9Q GAIN WILD-TYPE                                                    139
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  9Q GAIN MUTATED                                                   8
  9Q GAIN WILD-TYPE                                                13
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                                  12
  9Q GAIN WILD-TYPE                                                                70
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  9Q GAIN MUTATED                                                    3
  9Q GAIN WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  9Q GAIN MUTATED                                                 17
  9Q GAIN WILD-TYPE                                               62
D18V9, multiclass
                                                                   clus
vv                                                                  9Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         24
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               17
                                                                   clus
vv                                                                  9Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 62
[1] 7 2
[1] TRUE
[1] "dimension of 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    65   4   1   3
  9Q GAIN WILD-TYPE 284  14  18  22
D18V10, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              65               284
  R1               4                14
  R2               1                18
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9Q GAIN MUTATED      15                         2
  9Q GAIN WILD-TYPE    73                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           0    47
  9Q GAIN WILD-TYPE                                         1   231
D18V12, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                                  15                73
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  47               231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  52
  9Q GAIN WILD-TYPE   3 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   52
  9Q GAIN WILD-TYPE    3  264
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              52               264
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    53  40
  10P GAIN WILD-TYPE 193 129
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                93                322 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                40                129 
$`10P GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-VQ-A94U TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-6456 
       47.05        21.99        26.93         6.61         4.08        17.29 
TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 
       13.68         9.17        40.21         9.21        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 
       18.15        28.73         0.69         9.60        29.42         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8682 
        2.20        15.58         7.40         5.39         9.21        32.58 
TCGA-BR-8683 TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
        9.86         0.72        32.52        13.51        20.65         1.15 
TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 
       21.44        13.18        12.76        12.53         7.17        12.39 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4300 TCGA-CG-4440 TCGA-CG-4472 
       12.30        12.43        11.61        20.02         4.01        12.00 
TCGA-CG-4477 TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 
       30.97         4.01        19.13        20.55        18.84        17.19 
TCGA-D7-6818 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A 
       12.36        21.14        16.44        11.31        15.65        19.96 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 
        0.62        72.23         3.48         1.51         5.92        22.32 
TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        0.76        24.26        24.20        22.75        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 
        6.58        12.95        23.84        21.17        33.40         3.45 
TCGA-IN-8663 TCGA-IN-A7NR TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS 
        3.39         6.51        37.64        18.21         6.08        11.05 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-VQ-A8DU TCGA-VQ-A8E3 TCGA-VQ-A8P5 
        8.61        16.67       122.30         5.46        21.73         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91U 
       46.26        12.79        64.57        14.33        21.83         1.71 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA6J 
        4.54        21.04        27.55 

$`10P GAIN WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       27.35        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        8.98        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       35.24        35.84        15.32         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 
       33.21        37.25        14.43        11.44        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        8.05         0.56        19.96         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       25.05         3.72        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        31.96        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.66         0.46        20.42        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 
       13.02        13.15        13.35        11.21        12.10        12.59 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH 
       12.82        12.43         6.31        11.31         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05        54.08        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 
       12.03         0.00         9.01        18.97         7.07         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96        65.10        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6522 
        7.99        25.71        12.66        20.91        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       18.21        14.66        20.91        14.27         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
       22.29         8.38         4.34         7.13         7.99        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 
       77.29        63.06        52.21        30.51        26.47        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       18.15        28.96        22.82        21.07        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.68         3.25        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.51        20.25         0.26         2.10        29.00        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
       14.07        15.68        36.36        18.81        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       13.35        19.53         6.44         6.74        12.59        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       36.95         3.72        19.73        14.04        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 
       74.53         4.60         9.24         5.13        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        18.48        43.36        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       30.97        34.29        16.31        22.19         2.50         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N 
       29.59        73.41        39.45        11.70        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       20.81        32.88        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       55.56         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       66.81         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        12.43        17.26         0.79 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.62               0.00 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            122.30             116.38 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             13.51              15.27 
[1] "0.6 - 122.3 (13.5)" "0.0 - 116.4 (15.3)"
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         0        6        6        5         8        16
  10P GAIN WILD-TYPE       2       10       35       27        32        40
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           1         21         13          7       10
  10P GAIN WILD-TYPE         2         60         50         32       34
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  6                 10
  STAGE IB                  6                 35
  STAGE II                  5                 27
  STAGE IIA                 8                 32
  STAGE IIB                16                 40
  STAGE III                 1                  2
  STAGE IIIA               21                 60
  STAGE IIIB               13                 50
  STAGE IIIC                7                 32
  STAGE IV                 10                 34
[1] 11  2
[1] 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     5  16  50  26
  10P GAIN WILD-TYPE  18  77 146  93
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                5                 18
  T2               16                 77
  T3               50                146
  T4               26                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10P GAIN MUTATED   31 23 22 19
  10P GAIN WILD-TYPE 99 96 64 69
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               31                 99
  N1               23                 96
  N2               22                 64
  N3               19                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    88   7
  10P GAIN WILD-TYPE 301  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     88    7
  10P GAIN WILD-TYPE  301   23
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               88                301
  1                7                 23
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    38  60
  10P GAIN WILD-TYPE 120 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     38   60
  10P GAIN WILD-TYPE  120  223
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               38                120
  MALE                 60                223
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    75  14
  10P GAIN WILD-TYPE 247  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     75   14
  10P GAIN WILD-TYPE  247   62
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                75                247
  YES               14                 62
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  10P GAIN MUTATED                                          2
  10P GAIN WILD-TYPE                                       11
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  10P GAIN MUTATED                                      13
  10P GAIN WILD-TYPE                                    59
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                       33
  10P GAIN WILD-TYPE                                                    130
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  10P GAIN MUTATED                                                   3
  10P GAIN WILD-TYPE                                                18
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                                  19
  10P GAIN WILD-TYPE                                                                63
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  10P GAIN MUTATED                                                    1
  10P GAIN WILD-TYPE                                                  7
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  10P GAIN MUTATED                                                 26
  10P GAIN WILD-TYPE                                               53
D19V9, multiclass
                                                                   clus
vv                                                                  10P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           13
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          33
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               19
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                26
                                                                   clus
vv                                                                  10P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             59
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           130
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  53
[1] 7 2
[1] TRUE
[1] "dimension of 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    80   2   6   5
  10P GAIN WILD-TYPE 269  16  13  20
D19V10, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               80                269
  R1                2                 16
  R2                6                 13
  RX                5                 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"
D19V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10P GAIN MUTATED      28                         5
  10P GAIN WILD-TYPE    60                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           1    54
  10P GAIN WILD-TYPE                                         0   224
D19V12, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                                   28                 60
  BLACK OR AFRICAN AMERICAN                                5                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   54                224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  75
  10P GAIN WILD-TYPE   5 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   75
  10P GAIN WILD-TYPE    5  241
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               75                241
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    36  28
  10Q GAIN WILD-TYPE 210 141
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                64                351 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                28                141 
$`10Q GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-VQ-A94U TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6564 
       47.05        21.99        26.93         4.08        17.29        26.10 
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8286 
        9.21        33.63        39.78        28.73         0.69        29.42 
TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8682 TCGA-BR-A4J1 TCGA-BR-A4J7 
        2.66        15.58         7.40        32.58         0.72        32.52 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       20.65         1.15        13.18        12.76        12.53         7.17 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 TCGA-CG-4472 TCGA-CG-4477 TCGA-D7-6519 
       12.39        15.39        20.02        12.00        30.97        20.55 
TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU 
       18.84        17.19        12.36        18.21        21.14        16.44 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A74A TCGA-F1-6875 TCGA-FP-7735 TCGA-HU-8238 
       11.24        11.31        19.96        72.23         3.48         1.51 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4H6 
       22.32         0.76        24.26        24.20        22.75        21.17 
TCGA-IN-7808 TCGA-IN-8663 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7BT 
        3.45         3.39        18.21         6.08        11.05         8.61 
TCGA-RD-A8MV TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PX TCGA-VQ-A8PY 
      122.30        21.73        46.26        12.79        64.57        14.33 
TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A928 
       21.83        20.81         4.54         5.72 

$`10Q GAIN WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       27.35        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 
       44.94        21.90        36.16        35.24        35.84        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        0.56        19.96         2.20         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        31.96         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8528 
       13.15        13.35        11.21        12.10        12.59        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.30        12.59        11.64        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.91        19.13        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 
       24.72        16.80        19.50        17.19        14.66        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       28.96        22.82        21.07        24.30         5.59        22.68 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       33.40        36.36        18.81        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A7C1 
        8.52        74.53         4.60         9.24         5.13        16.67 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31        22.19         2.50         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ 
        9.27        23.41        15.65        13.35        29.59        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       39.45        11.70        61.22        18.74        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         6.58        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.69               0.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            122.30             116.38 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             17.24              14.43 
[1] "0.7 - 122.3 (17.2)" "0.0 - 116.4 (14.4)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         0        5        4        6         2        10
  10Q GAIN WILD-TYPE       2       11       37       26        38        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           1         17          9          2        7
  10Q GAIN WILD-TYPE         2         64         54         37       37
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  5                 11
  STAGE IB                  4                 37
  STAGE II                  6                 26
  STAGE IIA                 2                 38
  STAGE IIB                10                 46
  STAGE III                 1                  2
  STAGE IIIA               17                 64
  STAGE IIIB                9                 54
  STAGE IIIC                2                 37
  STAGE IV                  7                 37
[1] 11  2
[1] 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     4  12  35  15
  10Q GAIN WILD-TYPE  19  81 161 104
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                4                 19
  T2               12                 81
  T3               35                161
  T4               15                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"
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED    21  15  19  10
  10Q GAIN WILD-TYPE 109 104  67  78
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               21                109
  N1               15                104
  N2               19                 67
  N3               10                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    62   3
  10Q GAIN WILD-TYPE 327  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     62    3
  10Q GAIN WILD-TYPE  327   27
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               62                327
  1                3                 27
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    26  41
  10Q GAIN WILD-TYPE 132 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     26   41
  10Q GAIN WILD-TYPE  132  242
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               26                132
  MALE                 41                242
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    49  13
  10Q GAIN WILD-TYPE 273  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     49   13
  10Q GAIN WILD-TYPE  273   63
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                49                273
  YES               13                 63
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  10Q GAIN MUTATED                                          2
  10Q GAIN WILD-TYPE                                       11
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  10Q GAIN MUTATED                                       9
  10Q GAIN WILD-TYPE                                    63
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                       21
  10Q GAIN WILD-TYPE                                                    142
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  10Q GAIN MUTATED                                                   2
  10Q GAIN WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                                  12
  10Q GAIN WILD-TYPE                                                                70
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  10Q GAIN MUTATED                                                    2
  10Q GAIN WILD-TYPE                                                  6
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  10Q GAIN MUTATED                                                 18
  10Q GAIN WILD-TYPE                                               61
D20V9, multiclass
                                                                   clus
vv                                                                  10Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          21
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                18
                                                                   clus
vv                                                                  10Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of 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    57   1   3   3
  10Q GAIN WILD-TYPE 292  17  16  22
D20V10, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               57                292
  R1                1                 17
  R2                3                 16
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED      16                         3
  10Q GAIN WILD-TYPE    72                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           1    39
  10Q GAIN WILD-TYPE                                         0   239
D20V12, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                                   16                 72
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   39                239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0  51
  10Q GAIN WILD-TYPE   5 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   51
  10Q GAIN WILD-TYPE    5  265
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               51                265
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    33  23
  11P GAIN WILD-TYPE 213 146
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                56                359 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                23                146 
$`11P GAIN MUTATED`
TCGA-FP-A8CX TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7901 
        0.23        11.01         9.67        13.87        35.24         3.45 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8296 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A4CQ 
       37.25        11.44        15.58        24.79        20.88        34.98 
TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MH 
       12.89        13.51        12.59        12.33        12.30        12.20 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-5722 TCGA-D7-6526 TCGA-D7-8576 TCGA-D7-A6F0 
       20.02        54.08         0.99        17.19        14.66        22.29 
TCGA-EQ-8122 TCGA-FP-7916 TCGA-FP-8099 TCGA-HU-8243 TCGA-HU-A4G2 TCGA-HU-A4HD 
        7.99        14.07        17.06         5.92        24.30        33.40 
TCGA-IN-A6RJ TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZI 
       12.46        10.62        11.70         5.56        37.64        74.53 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU 
        8.61        16.67       115.69         8.94        35.61         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PX 
       13.02        18.48        43.36        22.19         2.70        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-AA6A 
       14.33        32.88         1.71         9.50         9.73        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F 
       32.94        54.12 

$`11P GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        9.86        27.35        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 
        6.18         9.57         6.61        34.68        15.95        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
        9.07        29.56        33.21        14.43         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       19.96         2.20         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        7.53        26.73        31.96        32.58         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
       15.39        12.07        12.82        12.43         6.31        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       12.43        11.61         6.58        11.77        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02         7.99         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       26.43        11.24        11.31        11.44        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        19.53        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60         9.24        11.05         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA 
       40.64       116.38        71.38        57.44        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.79         0.92        48.79        13.25        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       16.31         2.50        12.79        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A 
       23.41        15.65        13.35        29.59        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V 
       11.70        21.83        61.22        18.74        20.81        42.64 
TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       60.85        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
       11.24        18.41        43.66        28.41        17.13        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.23               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            115.69             122.30 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             14.20              15.22 
[1] "0.2 - 115.7 (14.2)" "0.0 - 122.3 (15.2)"
[1] "hr=" "1"  
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         0        3        4        2         2        11
  11P GAIN WILD-TYPE       2       13       37       30        38        45
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           0         11         13          6        7
  11P GAIN WILD-TYPE         3         70         50         33       37
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 13
  STAGE IB                  4                 37
  STAGE II                  2                 30
  STAGE IIA                 2                 38
  STAGE IIB                11                 45
  STAGE III                 0                  3
  STAGE IIIA               11                 70
  STAGE IIIB               13                 50
  STAGE IIIC                6                 33
  STAGE IV                  7                 37
[1] 11  2
[1] 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     3   7  31  18
  11P GAIN WILD-TYPE  20  86 165 101
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                3                 20
  T2                7                 86
  T3               31                165
  T4               18                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P GAIN MUTATED    12  17  19  11
  11P GAIN WILD-TYPE 118 102  67  77
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               12                118
  N1               17                102
  N2               19                 67
  N3               11                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    54   4
  11P GAIN WILD-TYPE 335  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     54    4
  11P GAIN WILD-TYPE  335   26
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               54                335
  1                4                 26
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    22  40
  11P GAIN WILD-TYPE 136 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     22   40
  11P GAIN WILD-TYPE  136  243
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               22                136
  MALE                 40                243
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    40  15
  11P GAIN WILD-TYPE 282  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     40   15
  11P GAIN WILD-TYPE  282   61
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                40                282
  YES               15                 61
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  11P GAIN MUTATED                                          2
  11P GAIN WILD-TYPE                                       11
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  11P GAIN MUTATED                                       7
  11P GAIN WILD-TYPE                                    65
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                       22
  11P GAIN WILD-TYPE                                                    141
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  11P GAIN MUTATED                                                   1
  11P GAIN WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                                  17
  11P GAIN WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  11P GAIN MUTATED                                                    0
  11P GAIN WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  11P GAIN MUTATED                                                 13
  11P GAIN WILD-TYPE                                               66
D21V9, multiclass
                                                                   clus
vv                                                                  11P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               17
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                13
                                                                   clus
vv                                                                  11P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  66
[1] 7 2
[1] TRUE
[1] "dimension of 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    47   2   5   4
  11P GAIN WILD-TYPE 302  16  14  21
D21V10, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               47                302
  R1                2                 16
  R2                5                 14
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11P GAIN MUTATED      15                         3
  11P GAIN WILD-TYPE    73                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           1    36
  11P GAIN WILD-TYPE                                         0   242
D21V12, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   36                242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  40
  11P GAIN WILD-TYPE   4 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   40
  11P GAIN WILD-TYPE    4  276
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               40                276
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    41  27
  11Q GAIN WILD-TYPE 205 142
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                68                347 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                27                142 
$`11Q GAIN MUTATED`
TCGA-CG-4444 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-7704 
       47.05        11.01         9.44         9.67        13.87        35.24 
TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8296 TCGA-BR-8361 
        3.45        37.25        11.44         0.69        15.58        31.10 
TCGA-BR-8589 TCGA-BR-8686 TCGA-BR-A4IY TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A487 
       27.12        20.88        12.89        12.59        12.33        12.30 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5722 
       12.20        20.02        54.08        12.00        30.97         0.99 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-EQ-8122 
       17.19        15.22        14.66        11.24        22.29         7.99 
TCGA-F1-6875 TCGA-FP-8099 TCGA-HU-8243 TCGA-HU-A4G2 TCGA-HU-A4H5 TCGA-HU-A4HD 
       72.23        17.06         5.92        24.30        23.80        33.40 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 
        3.39        12.46         6.74        10.62        11.70         5.56 
TCGA-KB-A93H TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
       37.64        74.53         8.61        16.67       115.69         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE 
       35.61         5.46        13.02        18.48        43.36        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S 
        2.70        64.57        14.33        21.83        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        1.71         9.73         4.54        43.66        38.93        32.94 
TCGA-VQ-AA6F TCGA-ZQ-A9CR 
       54.12         0.79 

$`11Q GAIN WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        9.86        27.35        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       19.56         9.47         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       33.63        39.78        18.15        15.32        28.73         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       29.56        33.21        14.43        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58         9.86         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82        12.43         6.31        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       11.61         6.58        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        10.26        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.31        11.44        20.32 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL 
       15.68        36.36         3.45        18.81        18.38        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
       19.53         6.44        12.59         6.51        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         5.13       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       48.79        13.25        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       13.35        29.59        73.41        39.45        11.70        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       20.81        42.64        60.85         9.50        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
        2.01        55.43         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D 
        2.66        42.54        11.24        18.41        28.41        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.69               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            115.69             122.30 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             14.94              14.79 
[1] "0.7 - 115.7 (14.9)" "0.0 - 122.3 (14.8)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         0        4        6        2         2        14
  11Q GAIN WILD-TYPE       2       12       35       30        38        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           0         13         14          7        9
  11Q GAIN WILD-TYPE         3         68         49         32       35
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  4                 12
  STAGE IB                  6                 35
  STAGE II                  2                 30
  STAGE IIA                 2                 38
  STAGE IIB                14                 42
  STAGE III                 0                  3
  STAGE IIIA               13                 68
  STAGE IIIB               14                 49
  STAGE IIIC                7                 32
  STAGE IV                  9                 35
[1] 11  2
[1] 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     3  13  31  24
  11Q GAIN WILD-TYPE  20  80 165  95
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                3                 20
  T2               13                 80
  T3               31                165
  T4               24                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q GAIN MUTATED    16  20  23  11
  11Q GAIN WILD-TYPE 114  99  63  77
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               16                114
  N1               20                 99
  N2               23                 63
  N3               11                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    67   4
  11Q GAIN WILD-TYPE 322  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     67    4
  11Q GAIN WILD-TYPE  322   26
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               67                322
  1                4                 26
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    30  44
  11Q GAIN WILD-TYPE 128 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     30   44
  11Q GAIN WILD-TYPE  128  239
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               30                128
  MALE                 44                239
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    48  19
  11Q GAIN WILD-TYPE 274  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     48   19
  11Q GAIN WILD-TYPE  274   57
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                48                274
  YES               19                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  11Q GAIN MUTATED                                          1
  11Q GAIN WILD-TYPE                                       12
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  11Q GAIN MUTATED                                       7
  11Q GAIN WILD-TYPE                                    65
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                       26
  11Q GAIN WILD-TYPE                                                    137
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  11Q GAIN MUTATED                                                   1
  11Q GAIN WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                                  18
  11Q GAIN WILD-TYPE                                                                64
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  11Q GAIN MUTATED                                                    1
  11Q GAIN WILD-TYPE                                                  7
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  11Q GAIN MUTATED                                                 19
  11Q GAIN WILD-TYPE                                               60
D22V9, multiclass
                                                                   clus
vv                                                                  11Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          26
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                19
                                                                   clus
vv                                                                  11Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           137
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of 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    58   2   6   4
  11Q GAIN WILD-TYPE 291  16  13  21
D22V10, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               58                291
  R1                2                 16
  R2                6                 13
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11Q GAIN MUTATED      15                         4
  11Q GAIN WILD-TYPE    73                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           1    43
  11Q GAIN WILD-TYPE                                         0   235
D22V12, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                4                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   43                235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  46
  11Q GAIN WILD-TYPE   4 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   46
  11Q GAIN WILD-TYPE    4  270
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               46                270
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    60  28
  12P GAIN WILD-TYPE 186 141
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                88                327 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                141 
$`12P GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-B7-A5TK 
       47.05        21.99        22.98        79.07        16.24         9.47 
TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-7723 TCGA-BR-7959 
       39.12        32.78        12.16        40.21        28.73        33.21 
TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 
       29.59         2.20        31.10         0.26         0.95         3.32 
TCGA-BR-8381 TCGA-BR-8486 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5798 
        7.36        20.22         1.48         0.72         1.15        13.41 
TCGA-CD-5799 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CG-4300 TCGA-CG-5722 
       13.02        12.53        12.39        12.59        20.02         0.99 
TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6820 
       12.03        12.66        19.13        18.54        17.19        11.31 
TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       19.50         5.92        11.31        22.29        15.65         8.38 
TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-A4BF 
       19.96        11.38         3.48        19.53        22.29         5.52 
TCGA-FP-A9TM TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC 
        6.21         1.51        28.96        22.82        24.30         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       22.75        25.81         8.98         6.51         6.58        20.25 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR 
       33.40         3.45         3.39        12.46         6.44         6.74 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZI 
       15.75         2.53        63.62        37.64        18.21        74.53 
TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV 
        6.08        16.67         8.94         5.79        48.79        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A91A TCGA-VQ-A91E 
       18.48        21.73         7.73        22.19        39.45        21.83 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A928 TCGA-VQ-AA6K 
       20.81        42.64         5.72        12.43 

$`12P GAIN WILD-TYPE`
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 
        0.23        20.15         9.86        27.35        26.93        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
        2.66        19.96        15.58         7.40         6.18        13.08 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
       22.19        17.52        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        34.98        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
        5.13        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 
       12.76        12.59         7.17        12.33        12.30        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        25.71        20.91        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       12.79        12.36        12.33        24.72        16.80        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
       20.32         4.34         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       72.23        21.27        14.07        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       13.58         0.56        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       26.47         5.92        24.39        18.15        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH 
        0.76         5.59        24.26        22.68        24.20        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       21.37        29.98         0.10         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
       36.36        18.81        18.38        13.35        19.53        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93J 
        6.51        10.62        11.70        13.51         5.56        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A804 
        3.72        19.73        14.04        45.67         8.52         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 
       16.87        19.04         0.92         5.46        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       37.41        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       14.33        73.41        11.70        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O 
        2.01        55.43         4.54         6.58        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       38.93        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        17.26         0.79 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.26               0.00 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             79.07             122.30 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             14.53              14.79 
[1] "0.3 - 79.1 (14.5)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         0        3        7        4        12        14
  12P GAIN WILD-TYPE       2       13       34       28        28        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           1         20         12          7        8
  12P GAIN WILD-TYPE         2         61         51         32       36
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 13
  STAGE IB                  7                 34
  STAGE II                  4                 28
  STAGE IIA                12                 28
  STAGE IIB                14                 42
  STAGE III                 1                  2
  STAGE IIIA               20                 61
  STAGE IIIB               12                 51
  STAGE IIIC                7                 32
  STAGE IV                  8                 36
[1] 11  2
[1] 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     6  14  53  19
  12P GAIN WILD-TYPE  17  79 143 100
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                6                 17
  T2               14                 79
  T3               53                143
  T4               19                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P GAIN MUTATED    26  23  25  16
  12P GAIN WILD-TYPE 104  96  61  72
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               26                104
  N1               23                 96
  N2               25                 61
  N3               16                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    82   6
  12P GAIN WILD-TYPE 307  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     82    6
  12P GAIN WILD-TYPE  307   24
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               82                307
  1                6                 24
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    31  61
  12P GAIN WILD-TYPE 127 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     31   61
  12P GAIN WILD-TYPE  127  222
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               31                127
  MALE                 61                222
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    69  16
  12P GAIN WILD-TYPE 253  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     69   16
  12P GAIN WILD-TYPE  253   60
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                69                253
  YES               16                 60
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  12P GAIN MUTATED                                          2
  12P GAIN WILD-TYPE                                       11
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  12P GAIN MUTATED                                      18
  12P GAIN WILD-TYPE                                    54
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                       27
  12P GAIN WILD-TYPE                                                    136
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  12P GAIN MUTATED                                                   5
  12P GAIN WILD-TYPE                                                16
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                                  15
  12P GAIN WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  12P GAIN MUTATED                                                    1
  12P GAIN WILD-TYPE                                                  7
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  12P GAIN MUTATED                                                 22
  12P GAIN WILD-TYPE                                               57
D23V9, multiclass
                                                                   clus
vv                                                                  12P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           18
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          27
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               15
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                22
                                                                   clus
vv                                                                  12P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             54
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           136
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of 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    77   4   4   1
  12P GAIN WILD-TYPE 272  14  15  24
D23V10, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               77                272
  R1                4                 14
  R2                4                 15
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12P GAIN MUTATED      20                         3
  12P GAIN WILD-TYPE    68                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           0    57
  12P GAIN WILD-TYPE                                         1   221
D23V12, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                                   20                 68
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   57                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     2  68
  12P GAIN WILD-TYPE   3 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   68
  12P GAIN WILD-TYPE    3  248
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               68                248
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    51  25
  12Q GAIN WILD-TYPE 195 144
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                76                339 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                25                144 
$`12Q GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-B7-A5TK TCGA-BR-4267 TCGA-BR-6563 
       47.05        21.99        79.07         9.47         6.18        39.12 
TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8295 
       32.78        12.16        28.73        33.21        29.59         2.20 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8381 TCGA-BR-8589 TCGA-BR-A4CS 
        0.26         0.95         3.32         7.36        27.12         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-8526 TCGA-CD-8530 
        0.72         0.53        13.41        13.02        12.53        12.39 
TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4472 TCGA-CG-5722 TCGA-D7-5578 
       12.82        12.30        12.43        12.00         0.99        12.66 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-8573 TCGA-D7-A4YV 
       19.13        18.54        17.19        10.26        19.50         5.92 
TCGA-D7-A747 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-A4BF 
        8.38        19.96        11.38        14.07        22.29         5.52 
TCGA-FP-A9TM TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC 
        6.21         1.51        28.96        22.82        24.30         3.25 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 
       22.75         8.98         6.51         6.58        20.25        23.84 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-AB1V TCGA-IP-7968 
       33.40         3.45         3.39        12.46        15.75         2.53 
TCGA-KB-A6F7 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N6 TCGA-SW-A7EB 
       63.62        74.53         6.08        16.67         8.94         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PY TCGA-VQ-A91E 
       48.79         7.73        22.19         2.70        14.33        21.83 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A928 
       20.81        42.64         9.50         5.72 

$`12Q GAIN WILD-TYPE`
TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       22.98        16.24         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       26.93        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         9.67         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       19.33        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       18.15        15.32         3.45         9.07        29.56        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        0.56        29.42         2.66        19.96        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        6.18        31.10        13.08        22.19        17.52        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 
        4.31        14.04        11.80        31.27        14.79        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
       27.55        28.57        12.89         8.98        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 
        1.15        21.44        16.14         5.13        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       13.35        11.21        12.10        12.76        12.59         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.43         6.31        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        25.71        20.91 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 
       20.55        18.84        18.61        17.85        13.35        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       21.27         3.48        19.53        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       13.58         0.56        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       26.47         5.92        24.39        18.15        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF 
        0.76         5.59        24.26        22.68        24.20        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 
       11.77        21.37        29.98         0.10         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       36.36        18.81        18.38        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        11.70        13.51 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       45.67        18.21         8.52         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        0.92         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       46.26        16.31         2.50        12.79        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       73.41        39.45        11.70        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        1.71        60.85         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         4.54         6.58        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.26               0.00 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             79.07             122.30 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            12.495             15.650 
[1] "0.3 - 79.1 (12.5)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0        2        4        5         9        12
  12Q GAIN WILD-TYPE       2       14       37       27        31        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           1         16         12          4        9
  12Q GAIN WILD-TYPE         2         65         51         35       35
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 14
  STAGE IB                  4                 37
  STAGE II                  5                 27
  STAGE IIA                 9                 31
  STAGE IIB                12                 44
  STAGE III                 1                  2
  STAGE IIIA               16                 65
  STAGE IIIB               12                 51
  STAGE IIIC                4                 35
  STAGE IV                  9                 35
[1] 11  2
[1] 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     4  12  43  19
  12Q GAIN WILD-TYPE  19  81 153 100
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                4                 19
  T2               12                 81
  T3               43                153
  T4               19                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q GAIN MUTATED    19  21  24  12
  12Q GAIN WILD-TYPE 111  98  62  76
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               19                111
  N1               21                 98
  N2               24                 62
  N3               12                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    69   6
  12Q GAIN WILD-TYPE 320  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     69    6
  12Q GAIN WILD-TYPE  320   24
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               69                320
  1                6                 24
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    25  53
  12Q GAIN WILD-TYPE 133 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     25   53
  12Q GAIN WILD-TYPE  133  230
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               25                133
  MALE                 53                230
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    60  12
  12Q GAIN WILD-TYPE 262  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     60   12
  12Q GAIN WILD-TYPE  262   64
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                60                262
  YES               12                 64
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  12Q GAIN MUTATED                                          1
  12Q GAIN WILD-TYPE                                       12
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  12Q GAIN MUTATED                                      18
  12Q GAIN WILD-TYPE                                    54
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                       22
  12Q GAIN WILD-TYPE                                                    141
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  12Q GAIN MUTATED                                                   3
  12Q GAIN WILD-TYPE                                                18
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                                  12
  12Q GAIN WILD-TYPE                                                                70
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  12Q GAIN MUTATED                                                    2
  12Q GAIN WILD-TYPE                                                  6
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  12Q GAIN MUTATED                                                 19
  12Q GAIN WILD-TYPE                                               60
D24V9, multiclass
                                                                   clus
vv                                                                  12Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           18
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                19
                                                                   clus
vv                                                                  12Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             54
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of 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    62   3   4   2
  12Q GAIN WILD-TYPE 287  15  15  23
D24V10, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               62                287
  R1                3                 15
  R2                4                 15
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12Q GAIN MUTATED      23                         1
  12Q GAIN WILD-TYPE    65                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           0    43
  12Q GAIN WILD-TYPE                                         1   235
D24V12, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                                   23                 65
  BLACK OR AFRICAN AMERICAN                                1                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   43                235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  59
  12Q GAIN WILD-TYPE   3 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   59
  12Q GAIN WILD-TYPE    3  257
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               59                257
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    90  53
  13Q GAIN WILD-TYPE 156 116
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               143                272 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                53                116 
$`13Q GAIN MUTATED`
TCGA-CG-4444 TCGA-MX-A663 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 
       47.05         9.86        11.70        11.01         9.44         4.64 
TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-6565 
        9.67         9.57         6.61        15.95        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7717 
       32.78        25.61        40.21         9.21        35.24        18.15 
TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8362 
       28.73         0.69        29.59         9.60        29.42        13.08 
TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8678 
       14.79        25.05         5.39         9.21        12.79        24.79 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4J1 
       32.58        20.88         8.22        10.68        13.87         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       14.17        28.34        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8529 
        1.15         5.13        13.02        13.15        12.59        12.30 
TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4305 
       12.82        12.43         6.58        12.20        20.02        15.95 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5730 
        7.99        54.08         7.07        12.00         1.02         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 
       69.04         7.99        25.71        12.66        19.13        18.54 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       17.85        17.19        10.26        15.98        12.36        11.31 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6F0 
       19.50        17.19        14.27        14.76        11.24        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7829 
       15.65         8.38         0.62         7.99        72.23        19.53 
TCGA-FP-A4BF TCGA-HF-7134 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 
        5.52        52.21        18.15        28.96        22.82        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       22.68        22.75        25.81         6.51         6.58         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RL 
       29.00        23.84        23.80        33.40        18.38        13.35 
TCGA-IN-A6RP TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7O7 
        6.44        11.70         5.56        37.64        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 
       18.21         8.52         8.61       122.30        37.91       115.69 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
       57.44         8.94        35.61         5.79        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
       13.25        13.02        21.73        37.41        22.19         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       17.85        23.41        13.35        14.33        73.41        39.45 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A922 TCGA-VQ-A94O 
       20.81        32.88         1.71        42.64         9.04        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-VQ-AA6K 
       42.54        11.24        32.94        27.55        12.43 

$`13Q GAIN WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK 
       27.35        26.93        58.03        26.70        19.56         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 
        4.08         9.34         6.18        34.68        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       13.68        19.33        26.10        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        8.98        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       35.84        33.63        39.78        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8081 
       29.56        33.21        37.25        14.43        11.44        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
       31.27         7.36         3.72        25.18        20.22         1.12 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       31.96         9.86        34.13         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 
        1.48        27.55        28.57        12.89         8.98         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 
        0.66        32.52        21.44        16.14        13.41        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.35        11.21        12.10        12.76        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI 
       12.43         6.31        12.30        11.31        11.61        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 
       12.62         3.02        27.02         1.02         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       18.97        30.97         6.97        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 
       21.07        20.91        20.55        18.84        18.61        13.35 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8575 
       15.22        12.79        12.33        24.72        16.80        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 
       13.78        26.43        11.31        11.44        20.32         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       19.96         7.13        14.47        21.27        11.38         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 
        0.56         6.21        77.29        63.06        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        1.51         5.92        24.39        22.32        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.30         5.59        24.20         3.25        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
       29.98         8.98         0.10        20.25         2.10        12.95 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39        12.46        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J 
       10.62        15.75        13.51         2.53        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        3.72        19.73        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         5.13        16.67        40.64       116.38        71.38 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P2 
       16.87        19.04         0.92        18.48        43.36        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50        12.79         1.87         9.27        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91W 
       64.57        11.70        21.83        61.22        18.74        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50         9.73        55.56         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 
        6.58         5.72        66.81         2.66        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        17.13        54.12        26.04        16.14 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.26               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            122.30             116.38 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             14.76              15.12 
[1] "0.3 - 122.3 (14.8)" "0.0 - 116.4 (15.1)"
[1] "hr=" "1.2"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         1        4        9       11        15        21
  13Q GAIN WILD-TYPE       1       12       32       21        25        35
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           1         30         22         11       19
  13Q GAIN WILD-TYPE         2         51         41         28       25
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  4                 12
  STAGE IB                  9                 32
  STAGE II                 11                 21
  STAGE IIA                15                 25
  STAGE IIB                21                 35
  STAGE III                 1                  2
  STAGE IIIA               30                 51
  STAGE IIIB               22                 41
  STAGE IIIC               11                 28
  STAGE IV                 19                 25
[1] 11  2
[1] 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     5  36  67  40
  13Q GAIN WILD-TYPE  18  57 129  79
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                5                 18
  T2               36                 57
  T3               67                129
  T4               40                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  13Q GAIN MUTATED   40 41 33 31
  13Q GAIN WILD-TYPE 90 78 53 57
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               40                 90
  N1               41                 78
  N2               33                 53
  N3               31                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   140  10
  13Q GAIN WILD-TYPE 249  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    140   10
  13Q GAIN WILD-TYPE  249   20
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0              140                249
  1               10                 20
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    48 105
  13Q GAIN WILD-TYPE 110 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     48  105
  13Q GAIN WILD-TYPE  110  178
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               48                110
  MALE                105                178
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   110  27
  13Q GAIN WILD-TYPE 212  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    110   27
  13Q GAIN WILD-TYPE  212   49
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO               110                212
  YES               27                 49
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  13Q GAIN MUTATED                                          4
  13Q GAIN WILD-TYPE                                        9
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  13Q GAIN MUTATED                                      18
  13Q GAIN WILD-TYPE                                    54
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                       54
  13Q GAIN WILD-TYPE                                                    109
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  13Q GAIN MUTATED                                                  10
  13Q GAIN WILD-TYPE                                                11
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                                  31
  13Q GAIN WILD-TYPE                                                                51
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  13Q GAIN MUTATED                                                    5
  13Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  13Q GAIN MUTATED                                                 30
  13Q GAIN WILD-TYPE                                               49
D25V9, multiclass
                                                                   clus
vv                                                                  13Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           18
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          54
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               31
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                30
                                                                   clus
vv                                                                  13Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             54
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           109
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 51
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  49
[1] 7 2
[1] TRUE
[1] "dimension of 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   118   8   6   9
  13Q GAIN WILD-TYPE 231  10  13  16
D25V10, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0              118                231
  R1                8                 10
  R2                6                 13
  RX                9                 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"
D25V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  13Q GAIN MUTATED      31                         6
  13Q GAIN WILD-TYPE    57                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           1    93
  13Q GAIN WILD-TYPE                                         0   185
D25V12, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                                   31                 57
  BLACK OR AFRICAN AMERICAN                                6                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   93                185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1 111
  13Q GAIN WILD-TYPE   4 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1  111
  13Q GAIN WILD-TYPE    4  205
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO              111                205
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    12  14
  14Q GAIN WILD-TYPE 234 155
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                26                389 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                14                155 
$`14Q GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-BR-4187 TCGA-BR-6705 TCGA-BR-8060 TCGA-BR-8295 
       47.05        21.99         4.64        25.61        11.44         2.20 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-CD-A48A TCGA-D7-6518 TCGA-D7-A6F2 TCGA-EQ-5647 
       13.51        20.42        12.43        19.13        15.65         0.62 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-IN-A6RI TCGA-IN-A7NR TCGA-IN-A7NT TCGA-R5-A7O7 
        5.52         5.92        18.38         6.51        10.62        45.67 
TCGA-R5-A7ZF TCGA-RD-A7BS TCGA-VQ-A8PE TCGA-VQ-A91V TCGA-VQ-A925 TCGA-VQ-A94R 
        8.52        11.05        22.19        42.64         4.54        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA6I 
       43.66        16.14 

$`14Q GAIN WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       27.35        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         6.97         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        0.56        29.42         2.66        19.96        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52         0.46        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        12.30        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        20.91        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
       22.29         8.38         4.34        19.96         7.13         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.44         6.74        12.59        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
        2.53         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       19.73        14.04        18.21        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       46.26        16.31         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       61.22        18.74        20.81        32.88         1.71        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        55.56         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T 
        6.58         5.72        66.81        21.04         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        27.55        12.43        17.26         0.79 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.62               0.00 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             47.05             122.30 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             14.58              14.79 
[1] "0.6 - 47.0 (14.6)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.4"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         1        1        2        0         1         3
  14Q GAIN WILD-TYPE       1       15       39       32        39        53
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           0          6          4          3        5
  14Q GAIN WILD-TYPE         3         75         59         36       39
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  1                 15
  STAGE IB                  2                 39
  STAGE II                  0                 32
  STAGE IIA                 1                 39
  STAGE IIB                 3                 53
  STAGE III                 0                  3
  STAGE IIIA                6                 75
  STAGE IIIB                4                 59
  STAGE IIIC                3                 36
  STAGE IV                  5                 39
[1] 11  2
[1] 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     2   5  12   8
  14Q GAIN WILD-TYPE  21  88 184 111
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                2                 21
  T2                5                 88
  T3               12                184
  T4                8                111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q GAIN MUTATED     6   5   6  10
  14Q GAIN WILD-TYPE 124 114  80  78
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                6                124
  N1                5                114
  N2                6                 80
  N3               10                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    23   5
  14Q GAIN WILD-TYPE 366  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     23    5
  14Q GAIN WILD-TYPE  366   25
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               23                366
  1                5                 25
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    12  16
  14Q GAIN WILD-TYPE 146 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     12   16
  14Q GAIN WILD-TYPE  146  267
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               12                146
  MALE                 16                267
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    21   7
  14Q GAIN WILD-TYPE 301  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     21    7
  14Q GAIN WILD-TYPE  301   69
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                21                301
  YES                7                 69
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  14Q GAIN MUTATED                                          1
  14Q GAIN WILD-TYPE                                       12
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  14Q GAIN MUTATED                                       3
  14Q GAIN WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                       13
  14Q GAIN WILD-TYPE                                                    150
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  14Q GAIN MUTATED                                                   0
  14Q GAIN WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                                   3
  14Q GAIN WILD-TYPE                                                                79
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  14Q GAIN MUTATED                                                    0
  14Q GAIN WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  14Q GAIN MUTATED                                                  8
  14Q GAIN WILD-TYPE                                               71
D26V9, multiclass
                                                                   clus
vv                                                                  14Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 8
                                                                   clus
vv                                                                  14Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 79
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  71
[1] 7 2
[1] TRUE
[1] "dimension of 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   2   3   1
  14Q GAIN WILD-TYPE 330  16  16  24
D26V10, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               19                330
  R1                2                 16
  R2                3                 16
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  14Q GAIN MUTATED       3                         1
  14Q GAIN WILD-TYPE    85                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           0    21
  14Q GAIN WILD-TYPE                                         1   257
D26V12, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                                    3                 85
  BLACK OR AFRICAN AMERICAN                                1                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   21                257
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  19
  14Q GAIN WILD-TYPE   4 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   19
  14Q GAIN WILD-TYPE    4  297
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               19                297
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    16  20
  15Q GAIN WILD-TYPE 230 149
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                36                379 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                20                149 
$`15Q GAIN MUTATED`
TCGA-CG-5727 TCGA-BR-4183 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7959 TCGA-BR-8683 
       79.07         6.61        12.16         9.21        33.21         9.86 
TCGA-BR-8687 TCGA-BR-A4J4 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-A486 
        8.22         0.53         1.15        13.02        12.59         6.31 
TCGA-CG-4477 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6815 TCGA-EQ-5647 TCGA-F1-6875 
       30.97        18.84        13.35        15.98         0.62        72.23 
TCGA-F1-A72C TCGA-FP-8099 TCGA-HU-A4GH TCGA-IN-7808 TCGA-IN-8663 TCGA-KB-A6F7 
       11.38        17.06        11.77         3.45         3.39        63.62 
TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV TCGA-VQ-A8DZ 
       37.64        18.21         6.08         8.61       122.30        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A925 
       18.48        46.26        12.79         2.70        17.85         4.54 

$`15Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        9.86        27.35        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45         9.07        29.56        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        31.96        32.58        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
       21.44        16.14         5.13        13.41        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.35        11.21        12.10        12.76        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82        12.43        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       20.55        18.54        18.61        17.85        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.99        14.47        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       21.17        14.07        15.68        33.40        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53         5.56        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       45.67         8.52        74.53         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 
        5.79         0.92        48.79         5.46        13.25        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO 
       34.29        16.31        22.19         2.50         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.73        55.56         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        5.72        66.81        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.53               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            122.30             116.38 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             12.69              15.39 
[1] "0.5 - 122.3 (12.7)" "0.0 - 116.4 (15.4)"
[1] "hr=" "1.5"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         0        3        2        3         3         3
  15Q GAIN WILD-TYPE       2       13       39       29        37        53
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           1          9          7          2        5
  15Q GAIN WILD-TYPE         2         72         56         37       39
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 13
  STAGE IB                  2                 39
  STAGE II                  3                 29
  STAGE IIA                 3                 37
  STAGE IIB                 3                 53
  STAGE III                 1                  2
  STAGE IIIA                9                 72
  STAGE IIIB                7                 56
  STAGE IIIC                2                 37
  STAGE IV                  5                 39
[1] 11  2
[1] 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     3   7  19  10
  15Q GAIN WILD-TYPE  20  86 177 109
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                3                 20
  T2                7                 86
  T3               19                177
  T4               10                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q GAIN MUTATED     9   7  14   8
  15Q GAIN WILD-TYPE 121 112  72  80
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                9                121
  N1                7                112
  N2               14                 72
  N3                8                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    33   5
  15Q GAIN WILD-TYPE 356  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     33    5
  15Q GAIN WILD-TYPE  356   25
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               33                356
  1                5                 25
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    12  27
  15Q GAIN WILD-TYPE 146 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     12   27
  15Q GAIN WILD-TYPE  146  256
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               12                146
  MALE                 27                256
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    29   7
  15Q GAIN WILD-TYPE 293  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     29    7
  15Q GAIN WILD-TYPE  293   69
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                29                293
  YES                7                 69
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  15Q GAIN MUTATED                                          2
  15Q GAIN WILD-TYPE                                       11
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  15Q GAIN MUTATED                                       4
  15Q GAIN WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                       12
  15Q GAIN WILD-TYPE                                                    151
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  15Q GAIN MUTATED                                                   2
  15Q GAIN WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                                   9
  15Q GAIN WILD-TYPE                                                                73
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  15Q GAIN MUTATED                                                    0
  15Q GAIN WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  15Q GAIN MUTATED                                                 10
  15Q GAIN WILD-TYPE                                               69
D27V9, multiclass
                                                                   clus
vv                                                                  15Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                9
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                10
                                                                   clus
vv                                                                  15Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 73
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  69
[1] 7 2
[1] TRUE
[1] "dimension of 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    24   3   6   1
  15Q GAIN WILD-TYPE 325  15  13  24
D27V10, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               24                325
  R1                3                 15
  R2                6                 13
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  15Q GAIN MUTATED       9                         4
  15Q GAIN WILD-TYPE    79                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           1    19
  15Q GAIN WILD-TYPE                                         0   259
D27V12, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                                    9                 79
  BLACK OR AFRICAN AMERICAN                                4                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   19                259
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  26
  15Q GAIN WILD-TYPE   5 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   26
  15Q GAIN WILD-TYPE    5  290
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               26                290
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    31  23
  16P GAIN WILD-TYPE 215 146
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                54                361 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                146 
$`16P GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX TCGA-B7-A5TJ TCGA-B7-A5TN 
       47.05        21.99        22.98         0.23        11.01         9.44 
TCGA-BR-4187 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-8080 TCGA-BR-8484 
        4.64         9.67        17.29         9.17         9.60        25.18 
TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-CD-5801 
       20.22         7.53        28.34        13.51        20.65        13.18 
TCGA-CD-5804 TCGA-CD-8528 TCGA-CD-8529 TCGA-CG-4438 TCGA-CG-4462 TCGA-CG-4472 
       12.10        12.33        12.30        54.08         0.00        12.00 
TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6817 
        1.02         0.99         4.01        18.54        17.19        12.79 
TCGA-D7-6818 TCGA-D7-8576 TCGA-D7-A747 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       12.36        14.66         8.38         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8249 TCGA-HU-A4GP TCGA-HU-A4GY TCGA-IN-8663 
       17.06         0.56        28.96         8.98         0.26         3.39 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-R5-A7ZE TCGA-RD-A7BT 
       13.35         6.44        10.62        11.70        18.21         8.61 
TCGA-VQ-A8PS TCGA-VQ-A925 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6K 
       13.35         4.54        32.94        54.12        16.14        12.43 

$`16P GAIN WILD-TYPE`
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07        16.24        20.15         9.86        27.35        26.93 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 
       58.03        26.70        11.70        19.56         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.87        13.68        19.33        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        5.39         9.21         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52         0.46        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 
       12.76        12.59        12.53         7.17        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99         8.05         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
        6.97        36.00         0.99         6.02       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        10.26        15.22        15.98 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        22.29        15.65         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       11.38        19.53        59.54         5.03        13.58         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
       29.98         0.10         6.51         6.58        20.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
       15.68        33.40        36.36         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
       12.46        19.53         6.74        12.59         6.51        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       57.44         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        0.92        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        9.04         2.01        55.43         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 
       28.41        38.93        17.13        26.04        27.55        17.26 
TCGA-ZQ-A9CR 
        0.79 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               0.0                0.1 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             54.12             122.30 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            12.345             15.750 
[1] "0.0 - 54.1 (12.3)"  "0.1 - 122.3 (15.8)"
[1] "hr=" "1.4"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         0        2        2        0         3        10
  16P GAIN WILD-TYPE       2       14       39       32        37        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           0         16          5          6       10
  16P GAIN WILD-TYPE         3         65         58         33       34
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 14
  STAGE IB                  2                 39
  STAGE II                  0                 32
  STAGE IIA                 3                 37
  STAGE IIB                10                 46
  STAGE III                 0                  3
  STAGE IIIA               16                 65
  STAGE IIIB                5                 58
  STAGE IIIC                6                 33
  STAGE IV                 10                 34
[1] 11  2
[1] 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     3  10  23  20
  16P GAIN WILD-TYPE  20  83 173  99
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                3                 20
  T2               10                 83
  T3               23                173
  T4               20                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P GAIN MUTATED    11  17  12  14
  16P GAIN WILD-TYPE 119 102  74  74
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               11                119
  N1               17                102
  N2               12                 74
  N3               14                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    45   6
  16P GAIN WILD-TYPE 344  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     45    6
  16P GAIN WILD-TYPE  344   24
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               45                344
  1                6                 24
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    20  38
  16P GAIN WILD-TYPE 138 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     20   38
  16P GAIN WILD-TYPE  138  245
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               20                138
  MALE                 38                245
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    38  11
  16P GAIN WILD-TYPE 284  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     38   11
  16P GAIN WILD-TYPE  284   65
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                38                284
  YES               11                 65
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  16P GAIN MUTATED                                          2
  16P GAIN WILD-TYPE                                       11
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  16P GAIN MUTATED                                       9
  16P GAIN WILD-TYPE                                    63
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                       23
  16P GAIN WILD-TYPE                                                    140
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  16P GAIN MUTATED                                                   3
  16P GAIN WILD-TYPE                                                18
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                                  12
  16P GAIN WILD-TYPE                                                                70
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  16P GAIN MUTATED                                                    0
  16P GAIN WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  16P GAIN MUTATED                                                  7
  16P GAIN WILD-TYPE                                               72
D28V9, multiclass
                                                                   clus
vv                                                                  16P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 7
                                                                   clus
vv                                                                  16P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           140
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  72
[1] 7 2
[1] TRUE
[1] "dimension of 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    44   1   6   3
  16P GAIN WILD-TYPE 305  17  13  22
D28V10, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               44                305
  R1                1                 17
  R2                6                 13
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16P GAIN MUTATED      11                         1
  16P GAIN WILD-TYPE    77                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           1    35
  16P GAIN WILD-TYPE                                         0   243
D28V12, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                                   11                 77
  BLACK OR AFRICAN AMERICAN                                1                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   35                243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  41
  16P GAIN WILD-TYPE   4 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   41
  16P GAIN WILD-TYPE    4  275
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               41                275
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    24  20
  16Q GAIN WILD-TYPE 222 149
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                44                371 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                20                149 
$`16Q GAIN MUTATED`
TCGA-CG-4460 TCGA-FP-A8CX TCGA-B7-A5TJ TCGA-BR-4187 TCGA-BR-4257 TCGA-BR-8486 
       21.99         0.23        11.01         4.64         9.67        20.22 
TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CD-5804 
        7.53         1.48        28.34        13.51        13.18        12.10 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CG-4438 TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-5719 
       12.33        12.30        54.08         0.00        12.00         1.02 
TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-6521 TCGA-D7-6818 TCGA-D7-8576 TCGA-EQ-8122 
        0.99         4.01        18.54        12.36        14.66         7.99 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8249 
        3.48        14.07        22.29        17.06         0.56        28.96 
TCGA-HU-A4GP TCGA-IN-8663 TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU 
        8.98         3.39         6.44         6.74        10.62        11.70 
TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-VQ-A8DV TCGA-VQ-A8PS TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.21         8.61        13.25        13.35        32.94        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6K 
       16.14        12.43 

$`16Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        79.07        16.24        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       27.35        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         6.97         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       34.13        13.87         6.08        34.98        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52         0.46        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       16.14         5.13        13.41        13.02        13.15        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 
       11.21        12.76        12.59        12.53         7.17        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
       30.97         6.97        36.00         0.99         6.02       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96        65.10        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8209 
       14.47        72.23        21.27        11.38        19.53        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       18.15        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       19.53        12.59         6.51        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.02        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        27.55        17.26         0.79 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               0.0                0.1 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             54.12             122.30 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             12.20              15.95 
[1] "0.0 - 54.1 (12.2)"  "0.1 - 122.3 (15.9)"
[1] "hr=" "1.6"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0        2        3        0         3         5
  16Q GAIN WILD-TYPE       2       14       38       32        37        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           0         10          5          6       10
  16Q GAIN WILD-TYPE         3         71         58         33       34
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 14
  STAGE IB                  3                 38
  STAGE II                  0                 32
  STAGE IIA                 3                 37
  STAGE IIB                 5                 51
  STAGE III                 0                  3
  STAGE IIIA               10                 71
  STAGE IIIB                5                 58
  STAGE IIIC                6                 33
  STAGE IV                 10                 34
[1] 11  2
[1] 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     3   8  20  15
  16Q GAIN WILD-TYPE  20  85 176 104
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                3                 20
  T2                8                 85
  T3               20                176
  T4               15                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"
                    vv
clus                  N0  N1  N2  N3
  16Q GAIN MUTATED    10  13   9  13
  16Q GAIN WILD-TYPE 120 106  77  75
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               10                120
  N1               13                106
  N2                9                 77
  N3               13                 75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    34   6
  16Q GAIN WILD-TYPE 355  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     34    6
  16Q GAIN WILD-TYPE  355   24
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               34                355
  1                6                 24
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    16  32
  16Q GAIN WILD-TYPE 142 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     16   32
  16Q GAIN WILD-TYPE  142  251
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               16                142
  MALE                 32                251
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    29  10
  16Q GAIN WILD-TYPE 293  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     29   10
  16Q GAIN WILD-TYPE  293   66
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                29                293
  YES               10                 66
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  16Q GAIN MUTATED                                          2
  16Q GAIN WILD-TYPE                                       11
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  16Q GAIN MUTATED                                       6
  16Q GAIN WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                       19
  16Q GAIN WILD-TYPE                                                    144
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  16Q GAIN MUTATED                                                   2
  16Q GAIN WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                                  14
  16Q GAIN WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  16Q GAIN MUTATED                                                    0
  16Q GAIN WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  16Q GAIN MUTATED                                                  4
  16Q GAIN WILD-TYPE                                               75
D29V9, multiclass
                                                                   clus
vv                                                                  16Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               14
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  16Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  75
[1] 7 2
[1] TRUE
[1] "dimension of 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    35   1   5   3
  16Q GAIN WILD-TYPE 314  17  14  22
D29V10, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               35                314
  R1                1                 17
  R2                5                 14
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16Q GAIN MUTATED      10                         1
  16Q GAIN WILD-TYPE    78                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           1    28
  16Q GAIN WILD-TYPE                                         0   250
D29V12, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                                   10                 78
  BLACK OR AFRICAN AMERICAN                                1                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   28                250
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  33
  16Q GAIN WILD-TYPE   4 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   33
  16Q GAIN WILD-TYPE    4  283
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               33                283
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    12  15
  17P GAIN WILD-TYPE 234 154
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                27                388 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                15                154 
$`17P GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-BR-8059 TCGA-BR-8686 TCGA-BR-A4QI 
       21.99        22.98        16.24        14.43        20.88        21.44 
TCGA-CG-4455 TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-6817 TCGA-D7-8573 TCGA-D7-A6EY 
       12.03         0.99        12.03        12.79        19.50        11.44 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7829 TCGA-HJ-7597 TCGA-HU-A4GF TCGA-HU-A4HD 
        0.62        72.23        19.53        26.47        25.81        33.40 
TCGA-MX-A666 TCGA-R5-A7ZR TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 
       14.04         6.08        55.56         9.04         2.01         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 
       21.04        42.54        43.66 

$`17P GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       47.05        79.07         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       26.93        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
       26.73        24.79        31.96        32.58         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65        20.42         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
       54.08         4.01        14.01        29.98        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 
       36.00         1.02         0.99         6.02       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         7.99        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       21.83        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 
       42.64        60.85         9.50         9.73        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
        5.72        66.81         2.66        11.24        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       38.93        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.62               0.00 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             72.23             122.30 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             19.50              14.71 
[1] "0.6 - 72.2 (19.5)"  "0.0 - 122.3 (14.7)"
[1] "hr=" "1.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         0        1        1        1         5         2
  17P GAIN WILD-TYPE       2       15       40       31        35        54
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           2          5          3          2        5
  17P GAIN WILD-TYPE         1         76         60         37       39
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 15
  STAGE IB                  1                 40
  STAGE II                  1                 31
  STAGE IIA                 5                 35
  STAGE IIB                 2                 54
  STAGE III                 2                  1
  STAGE IIIA                5                 76
  STAGE IIIB                3                 60
  STAGE IIIC                2                 37
  STAGE IV                  5                 39
[1] 11  2
[1] 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     0   5  15   9
  17P GAIN WILD-TYPE  23  88 181 110
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                0                 23
  T2                5                 88
  T3               15                181
  T4                9                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P GAIN MUTATED     6  10   4   6
  17P GAIN WILD-TYPE 124 109  82  82
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                6                124
  N1               10                109
  N2                4                 82
  N3                6                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    21   4
  17P GAIN WILD-TYPE 368  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     21    4
  17P GAIN WILD-TYPE  368   26
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               21                368
  1                4                 26
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     9  20
  17P GAIN WILD-TYPE 149 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      9   20
  17P GAIN WILD-TYPE  149  263
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                9                149
  MALE                 20                263
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    21   5
  17P GAIN WILD-TYPE 301  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     21    5
  17P GAIN WILD-TYPE  301   71
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                21                301
  YES                5                 71
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  17P GAIN MUTATED                                          1
  17P GAIN WILD-TYPE                                       12
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  17P GAIN MUTATED                                       1
  17P GAIN WILD-TYPE                                    71
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                        6
  17P GAIN WILD-TYPE                                                    157
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  17P GAIN MUTATED                                                   2
  17P GAIN WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                                   5
  17P GAIN WILD-TYPE                                                                77
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  17P GAIN MUTATED                                                    0
  17P GAIN WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  17P GAIN MUTATED                                                 12
  17P GAIN WILD-TYPE                                               67
D30V9, multiclass
                                                                   clus
vv                                                                  17P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                12
                                                                   clus
vv                                                                  17P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             71
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 77
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  67
[1] 7 2
[1] TRUE
[1] "dimension of 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    21   0   5   1
  17P GAIN WILD-TYPE 328  18  14  24
D30V10, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               21                328
  R1                0                 18
  R2                5                 14
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17P GAIN MUTATED       3                         3
  17P GAIN WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0    17
  17P GAIN WILD-TYPE                                         1   261
D30V12, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                                    3                 85
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   17                261
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  17
  17P GAIN WILD-TYPE   5 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   17
  17P GAIN WILD-TYPE    5  299
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               17                299
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    33  28
  17Q GAIN WILD-TYPE 213 141
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                61                354 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                28                141 
$`17Q GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-3M-AB46 TCGA-B7-5818 TCGA-BR-8059 
       21.99        22.98        16.24        58.03        11.70        14.43 
TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8369 TCGA-BR-8686 
       11.44        29.42         2.66        15.58        14.04        20.88 
TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-A486 TCGA-CD-A48A 
       12.89         0.53        20.42        21.44         6.31        12.43 
TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-6521 
        7.99        12.03         1.02         0.99        12.03        18.54 
TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-A6EY TCGA-D7-A6F0 
       13.35        12.79        19.50        14.66        11.44        22.29 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-7916 TCGA-HJ-7597 TCGA-HU-8604 
        0.62        72.23        19.53        14.07        26.47        22.82 
TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT 
       33.40        18.81        18.38        13.35         6.44        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-MX-A666 TCGA-R5-A7ZR TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       11.70        15.75        14.04         6.08        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8PM TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91Z 
       18.48         1.87        73.41        20.81        42.64        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        9.04         2.01         4.54        66.81        21.04        42.54 
TCGA-VQ-AA68 
       43.66 

$`17Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       47.05        79.07         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.93        26.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
        3.45         9.07        29.56        33.21        37.25         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       29.59         9.60        32.25         8.05         0.56        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       24.79        31.96        32.58         9.86         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       27.55        28.57         8.98         0.72        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF 
        0.66        32.52        13.51         0.46        20.65         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82        12.43        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        29.98        19.07         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02       105.07        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       20.91        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       12.33        24.72        16.80        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        26.43        11.24        11.31        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         7.99        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27        11.38         3.48        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       18.15        28.96        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       36.36         3.45         3.39        12.46        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       12.59         6.51        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64        36.95         3.72        19.73        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 
       19.04         5.79         0.92        48.79         5.46        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70        17.85         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        14.33        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        18.74        32.88         1.71        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T 
        9.73        55.43         6.58         5.72         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.53               0.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             73.41             122.30 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             14.43              15.12 
[1] "0.5 - 73.4 (14.4)"  "0.0 - 122.3 (15.1)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         1        3        8        3         7         6
  17Q GAIN WILD-TYPE       1       13       33       29        33        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           2          9          7          5       10
  17Q GAIN WILD-TYPE         1         72         56         34       34
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  3                 13
  STAGE IB                  8                 33
  STAGE II                  3                 29
  STAGE IIA                 7                 33
  STAGE IIB                 6                 50
  STAGE III                 2                  1
  STAGE IIIA                9                 72
  STAGE IIIB                7                 56
  STAGE IIIC                5                 34
  STAGE IV                 10                 34
[1] 11  2
[1] 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     4  17  26  17
  17Q GAIN WILD-TYPE  19  76 170 102
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                4                 19
  T2               17                 76
  T3               26                170
  T4               17                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q GAIN MUTATED    22  13  11  15
  17Q GAIN WILD-TYPE 108 106  75  73
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               22                108
  N1               13                106
  N2               11                 75
  N3               15                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    51   7
  17Q GAIN WILD-TYPE 338  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     51    7
  17Q GAIN WILD-TYPE  338   23
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               51                338
  1                7                 23
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    19  45
  17Q GAIN WILD-TYPE 139 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     19   45
  17Q GAIN WILD-TYPE  139  238
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               19                139
  MALE                 45                238
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    46  13
  17Q GAIN WILD-TYPE 276  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     46   13
  17Q GAIN WILD-TYPE  276   63
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                46                276
  YES               13                 63
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  17Q GAIN MUTATED                                          4
  17Q GAIN WILD-TYPE                                        9
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  17Q GAIN MUTATED                                       5
  17Q GAIN WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                       23
  17Q GAIN WILD-TYPE                                                    140
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  17Q GAIN MUTATED                                                   2
  17Q GAIN WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                                  12
  17Q GAIN WILD-TYPE                                                                70
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  17Q GAIN MUTATED                                                    0
  17Q GAIN WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  17Q GAIN MUTATED                                                 16
  17Q GAIN WILD-TYPE                                               63
D31V9, multiclass
                                                                   clus
vv                                                                  17Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                16
                                                                   clus
vv                                                                  17Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           140
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  63
[1] 7 2
[1] TRUE
[1] "dimension of 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    51   0   6   1
  17Q GAIN WILD-TYPE 298  18  13  24
D31V10, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               51                298
  R1                0                 18
  R2                6                 13
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17Q GAIN MUTATED       9                         5
  17Q GAIN WILD-TYPE    79                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    40
  17Q GAIN WILD-TYPE                                         1   238
D31V12, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                                    9                 79
  BLACK OR AFRICAN AMERICAN                                5                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   40                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1  41
  17Q GAIN WILD-TYPE   4 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   41
  17Q GAIN WILD-TYPE    4  275
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               41                275
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    43  36
  18P GAIN WILD-TYPE 203 133
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                79                336 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                36                133 
$`18P GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-4475 TCGA-MX-A663 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4257 
       21.99        22.98         9.86         6.97        18.35         9.67 
TCGA-BR-6565 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
        9.17        15.32         3.45        11.44         0.69         9.60 
TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8485 
        8.05         2.20        15.58         7.40        13.08         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8677 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4J1 
       20.22         1.12        26.73         8.22        13.87         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.51        20.65         1.15        13.41        13.02        13.15 
TCGA-CD-5804 TCGA-CD-A486 TCGA-CD-A4MH TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6526 
       12.10         6.31        12.20        12.03        20.91        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4YY TCGA-D7-A6EX 
       10.26        15.22        12.79        14.66        13.78        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       22.29        15.65        19.96         0.56         5.52         6.21 
TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF 
       63.06        26.47         5.92         0.76        22.75        25.81 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       23.80        33.40        18.38        19.53         6.44         6.74 
TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A666 TCGA-R5-A7ZI TCGA-RD-A8N9 TCGA-VQ-A8DL 
       10.62        63.62        14.04        74.53        35.61         0.92 
TCGA-VQ-A8E3 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       21.73        22.19         2.70        17.85         1.87         9.27 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6A 
       21.83        18.74         1.71         9.04        43.66        38.93 
TCGA-ZQ-A9CR 
        0.79 

$`18P GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       47.05        79.07        16.24         0.23        20.15        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       26.93        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.47         9.44         6.61         4.64         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       39.78        18.15        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
       37.25        14.43        29.59        32.25         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.66        19.96         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        5.39        25.18        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       20.88        10.68        34.13         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        28.34         0.66        32.52         0.46        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       21.44        16.14         5.13        13.18        13.35        11.21 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        13.35        15.98        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        36.43        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.24        11.44        20.32         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
       59.54         5.03        13.58        77.29        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       29.00        23.84        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RS 
        3.45        18.81         3.39        12.46        13.35        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64        36.95         3.72        19.73        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        5.79        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       43.36        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PP 
       34.29        46.26        16.31         2.50        12.79        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V 
       39.45        11.70        61.22        20.81        32.88        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 
       60.85         9.50         9.73        55.56         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       42.54        11.24        18.41        28.41        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.56               0.00 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             74.53             122.30 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            13.080             15.965 
[1] "0.6 - 74.5 (13.1)"  "0.0 - 122.3 (16.0)"
[1] "hr=" "1.4"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         1        2        7        5         9        10
  18P GAIN WILD-TYPE       1       14       34       27        31        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           0         13         10         13        9
  18P GAIN WILD-TYPE         3         68         53         26       35
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  2                 14
  STAGE IB                  7                 34
  STAGE II                  5                 27
  STAGE IIA                 9                 31
  STAGE IIB                10                 46
  STAGE III                 0                  3
  STAGE IIIA               13                 68
  STAGE IIIB               10                 53
  STAGE IIIC               13                 26
  STAGE IV                  9                 35
[1] 11  2
[1] 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     7  13  34  27
  18P GAIN WILD-TYPE  16  80 162  92
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                7                 16
  T2               13                 80
  T3               34                162
  T4               27                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P GAIN MUTATED    23  22  14  23
  18P GAIN WILD-TYPE 107  97  72  65
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               23                107
  N1               22                 97
  N2               14                 72
  N3               23                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    74   5
  18P GAIN WILD-TYPE 315  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     74    5
  18P GAIN WILD-TYPE  315   25
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               74                315
  1                5                 25
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    37  48
  18P GAIN WILD-TYPE 121 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     37   48
  18P GAIN WILD-TYPE  121  235
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               37                121
  MALE                 48                235
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    64  14
  18P GAIN WILD-TYPE 258  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     64   14
  18P GAIN WILD-TYPE  258   62
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                64                258
  YES               14                 62
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  18P GAIN MUTATED                                          4
  18P GAIN WILD-TYPE                                        9
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  18P GAIN MUTATED                                       6
  18P GAIN WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                       35
  18P GAIN WILD-TYPE                                                    128
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  18P GAIN MUTATED                                                   4
  18P GAIN WILD-TYPE                                                17
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                                  12
  18P GAIN WILD-TYPE                                                                70
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  18P GAIN MUTATED                                                    3
  18P GAIN WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  18P GAIN MUTATED                                                 20
  18P GAIN WILD-TYPE                                               59
D32V9, multiclass
                                                                   clus
vv                                                                  18P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          35
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                20
                                                                   clus
vv                                                                  18P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           128
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of 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    66   5   4   5
  18P GAIN WILD-TYPE 283  13  15  20
D32V10, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               66                283
  R1                5                 13
  R2                4                 15
  RX                5                 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"
D32V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED      15                         0
  18P GAIN WILD-TYPE    73                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           0    58
  18P GAIN WILD-TYPE                                         1   220
D32V12, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                0                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   58                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1  62
  18P GAIN WILD-TYPE   4 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   62
  18P GAIN WILD-TYPE    4  254
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               62                254
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    30  21
  18Q GAIN WILD-TYPE 216 148
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                51                364 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                21                148 
$`18Q GAIN MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6565 TCGA-BR-7901 TCGA-BR-8077 
       21.99         6.97         9.67         9.17         3.45         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 
        9.60         8.05         2.20        15.58         7.40        13.08 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD 
       25.18         1.12         1.48         0.72        13.51        20.65 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 TCGA-D7-5579 
        1.15        13.41        13.02        13.15        12.10        20.91 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-FP-8631 TCGA-FP-A4BF 
       15.22        12.79        13.78        11.31         0.56         5.52 
TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8610 TCGA-HU-A4GD 
       63.06        26.47         5.92        18.15         0.76        22.75 
TCGA-HU-A4GF TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN TCGA-MX-A666 
       25.81        23.80        33.40        18.38        19.53        14.04 
TCGA-R5-A7ZI TCGA-RD-A8N9 TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A91E 
       74.53        35.61         2.70         1.87         9.27        21.83 
TCGA-VQ-A91N TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       18.74        43.66         0.79 

$`18Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        9.86        27.35        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       17.29        13.68        19.33        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       11.44        29.59        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       19.96         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        34.98        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 
        0.46        20.42        21.44        16.14         5.13        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.35        11.21        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       13.35        17.19        10.26        15.98        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       36.43        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
        5.03        13.58         6.21        77.29        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.84        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81         3.39        12.46        13.35         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
        2.53         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       19.73        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK 
       46.26        16.31        22.19         2.50        12.79        17.85 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       73.41        39.45        11.70        61.22        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.56               0.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             74.53             122.30 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            13.080             15.665 
[1] "0.6 - 74.5 (13.1)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1.3"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         1        1        4        4         5         6
  18Q GAIN WILD-TYPE       1       15       37       28        35        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           0          9          5         10        7
  18Q GAIN WILD-TYPE         3         72         58         29       37
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  1                 15
  STAGE IB                  4                 37
  STAGE II                  4                 28
  STAGE IIA                 5                 35
  STAGE IIB                 6                 50
  STAGE III                 0                  3
  STAGE IIIA                9                 72
  STAGE IIIB                5                 58
  STAGE IIIC               10                 29
  STAGE IV                  7                 37
[1] 11  2
[1] 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     3   9  16  25
  18Q GAIN WILD-TYPE  20  84 180  94
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                3                 20
  T2                9                 84
  T3               16                180
  T4               25                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q GAIN MUTATED    16  11  10  15
  18Q GAIN WILD-TYPE 114 108  76  73
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               16                114
  N1               11                108
  N2               10                 76
  N3               15                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    45   4
  18Q GAIN WILD-TYPE 344  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     45    4
  18Q GAIN WILD-TYPE  344   26
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               45                344
  1                4                 26
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    24  31
  18Q GAIN WILD-TYPE 134 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     24   31
  18Q GAIN WILD-TYPE  134  252
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               24                134
  MALE                 31                252
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    42   7
  18Q GAIN WILD-TYPE 280  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     42    7
  18Q GAIN WILD-TYPE  280   69
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                42                280
  YES                7                 69
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  18Q GAIN MUTATED                                          4
  18Q GAIN WILD-TYPE                                        9
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  18Q GAIN MUTATED                                       5
  18Q GAIN WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                       20
  18Q GAIN WILD-TYPE                                                    143
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  18Q GAIN MUTATED                                                   4
  18Q GAIN WILD-TYPE                                                17
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                                   6
  18Q GAIN WILD-TYPE                                                                76
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  18Q GAIN MUTATED                                                    3
  18Q GAIN WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  18Q GAIN MUTATED                                                 13
  18Q GAIN WILD-TYPE                                               66
D33V9, multiclass
                                                                   clus
vv                                                                  18Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                13
                                                                   clus
vv                                                                  18Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 76
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  66
[1] 7 2
[1] TRUE
[1] "dimension of 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    43   3   3   3
  18Q GAIN WILD-TYPE 306  15  16  22
D33V10, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               43                306
  R1                3                 15
  R2                3                 16
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18Q GAIN MUTATED      13                         0
  18Q GAIN WILD-TYPE    75                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           0    35
  18Q GAIN WILD-TYPE                                         1   243
D33V12, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                                   13                 75
  BLACK OR AFRICAN AMERICAN                                0                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   35                243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1  43
  18Q GAIN WILD-TYPE   4 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   43
  18Q GAIN WILD-TYPE    4  273
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               43                273
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    32  16
  19P GAIN WILD-TYPE 214 153
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                48                367 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                16                153 
$`19P GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-B7-A5TK TCGA-BR-4253 
       47.05        21.99        22.98        16.24         9.47         4.08 
TCGA-BR-6456 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8370 TCGA-BR-A453 
       17.29        33.21        29.42        19.96         3.32         6.08 
TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 
       13.51        21.44        13.18        12.53        12.39        12.82 
TCGA-CD-A48C TCGA-CG-4449 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 
       11.61        19.07         0.99         4.01        25.71        19.13 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6528 TCGA-D7-8578 TCGA-D7-A4YU TCGA-FP-A4BF 
       20.55        18.54        15.22        21.14        16.44         5.52 
TCGA-HF-7133 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4H2 
       63.06        28.96        22.82        24.30        22.75        12.95 
TCGA-IN-7808 TCGA-IN-A6RP TCGA-MX-A666 TCGA-SW-A7EB TCGA-VQ-A8E3 TCGA-VQ-A8PE 
        3.45         6.44        14.04         5.79        21.73        22.19 
TCGA-VQ-A8PH TCGA-VQ-A91A TCGA-VQ-A91S TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-AA6I 
       12.79        39.45        32.88         4.54        66.81        16.14 

$`19P GAIN WILD-TYPE`
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07         0.23        20.15         9.86        27.35        26.93 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 
        9.60        32.25         8.05         0.56         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.30        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        29.98        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       28.96        65.10        69.04        21.07         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.91        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
       13.58         0.56         6.21        77.29        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        18.15        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40        36.36        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64        36.95         3.72        19.73        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.87        19.04         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        18.48        43.36        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       13.35        29.59        64.57        14.33        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       21.83        61.22        18.74        20.81         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        54.12        26.04        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.99               0.00 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             66.81             122.30 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            16.865             14.430 
[1] "1.0 - 66.8 (16.9)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         0        0        4        3         4         6
  19P GAIN WILD-TYPE       2       16       37       29        36        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           0         13         10          2        6
  19P GAIN WILD-TYPE         3         68         53         37       38
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 16
  STAGE IB                  4                 37
  STAGE II                  3                 29
  STAGE IIA                 4                 36
  STAGE IIB                 6                 50
  STAGE III                 0                  3
  STAGE IIIA               13                 68
  STAGE IIIB               10                 53
  STAGE IIIC                2                 37
  STAGE IV                  6                 38
[1] 11  2
[1] 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     1  14  29   8
  19P GAIN WILD-TYPE  22  79 167 111
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                1                 22
  T2               14                 79
  T3               29                167
  T4                8                111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19P GAIN MUTATED     9  18   8  15
  19P GAIN WILD-TYPE 121 101  78  73
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                9                121
  N1               18                101
  N2                8                 78
  N3               15                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    44   6
  19P GAIN WILD-TYPE 345  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     44    6
  19P GAIN WILD-TYPE  345   24
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               44                345
  1                6                 24
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    19  34
  19P GAIN WILD-TYPE 139 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     19   34
  19P GAIN WILD-TYPE  139  249
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               19                139
  MALE                 34                249
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    38  10
  19P GAIN WILD-TYPE 284  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     38   10
  19P GAIN WILD-TYPE  284   66
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                38                284
  YES               10                 66
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  19P GAIN MUTATED                                          2
  19P GAIN WILD-TYPE                                       11
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  19P GAIN MUTATED                                      10
  19P GAIN WILD-TYPE                                    62
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                       15
  19P GAIN WILD-TYPE                                                    148
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  19P GAIN MUTATED                                                   5
  19P GAIN WILD-TYPE                                                16
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                                   7
  19P GAIN WILD-TYPE                                                                75
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  19P GAIN MUTATED                                                    0
  19P GAIN WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  19P GAIN MUTATED                                                 12
  19P GAIN WILD-TYPE                                               67
D34V9, multiclass
                                                                   clus
vv                                                                  19P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           10
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                12
                                                                   clus
vv                                                                  19P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             62
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 75
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  67
[1] 7 2
[1] TRUE
[1] "dimension of 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    37   4   5   3
  19P GAIN WILD-TYPE 312  14  14  22
D34V10, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               37                312
  R1                4                 14
  R2                5                 14
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED      11                         1
  19P GAIN WILD-TYPE    77                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           0    32
  19P GAIN WILD-TYPE                                         1   246
D34V12, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                                   11                 77
  BLACK OR AFRICAN AMERICAN                                1                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   32                246
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  36
  19P GAIN WILD-TYPE   5 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   36
  19P GAIN WILD-TYPE    5  280
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               36                280
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    43  29
  19Q GAIN WILD-TYPE 203 140
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                72                343 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                29                140 
$`19Q GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-B7-A5TK TCGA-BR-4253 
       47.05        21.99        22.98        16.24         9.47         4.08 
TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8370 
       19.33        39.78        33.21        29.42        19.96         3.32 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8690 TCGA-BR-A453 TCGA-BR-A4J1 TCGA-BR-A4J8 
        9.21         1.12        10.68         6.08         0.72        13.51 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48C 
       13.18        12.76        12.53        12.39        12.82        11.61 
TCGA-CG-4438 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 
       54.08         0.99         4.01        25.71        19.13        18.54 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8578 TCGA-D7-A4YU TCGA-EQ-8122 
       12.36        12.33        24.72        21.14        16.44         7.99 
TCGA-F1-6875 TCGA-FP-7916 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8244 
       72.23        14.07         5.52         6.21        63.06        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H2 
       28.96        22.82        24.30        22.75         2.10        12.95 
TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-MX-A666 TCGA-R5-A7ZR 
        3.45        13.35         6.44        63.62        14.04         6.08 
TCGA-RD-A7BT TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8P5 
        8.61        35.61         5.79        13.25        21.73         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A91A TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A923 
       22.19        12.79        39.45        32.88         1.71         2.01 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6K 
        4.54        66.81        11.24        54.12        16.14        12.43 

$`19Q GAIN WILD-TYPE`
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07         0.23        20.15         9.86        27.35        26.93 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
       32.25         8.05         0.56         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
       17.52         0.95        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        20.88         8.22        34.13        13.87         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.59         7.17        12.33        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         6.02       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96        65.10        69.04        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       12.66        20.91        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       11.31        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       14.47        21.27        11.38         3.48        19.53        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 
       17.06        59.54         5.03        13.58         0.56        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 
       52.21        30.51        26.47         1.51         5.92        18.15 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.32        21.07         0.76         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40        36.36        18.81         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        45.67        18.21         8.52        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60         9.24        11.05         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        16.87        19.04         0.92        48.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        18.48        43.36        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       30.97        34.29        46.26        16.31         2.50         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        14.33        73.41        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        18.74        20.81        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73        55.56         9.04        55.43         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       21.04         2.66        42.54        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 
       38.93        32.94        17.13        26.04        27.55        17.26 
TCGA-ZQ-A9CR 
        0.79 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.72               0.00 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             72.23             122.30 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             13.30              15.39 
[1] "0.7 - 72.2 (13.3)"  "0.0 - 122.3 (15.4)"
[1] "hr=" "1"  
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         0        2        6        4         5         9
  19Q GAIN WILD-TYPE       2       14       35       28        35        47
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           1         19         13          6        8
  19Q GAIN WILD-TYPE         2         62         50         33       36
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 14
  STAGE IB                  6                 35
  STAGE II                  4                 28
  STAGE IIA                 5                 35
  STAGE IIB                 9                 47
  STAGE III                 1                  2
  STAGE IIIA               19                 62
  STAGE IIIB               13                 50
  STAGE IIIC                6                 33
  STAGE IV                  8                 36
[1] 11  2
[1] 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     4  17  42  14
  19Q GAIN WILD-TYPE  19  76 154 105
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                4                 19
  T2               17                 76
  T3               42                154
  T4               14                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q GAIN MUTATED    14  27  10  23
  19Q GAIN WILD-TYPE 116  92  76  65
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               14                116
  N1               27                 92
  N2               10                 76
  N3               23                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    68   6
  19Q GAIN WILD-TYPE 321  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     68    6
  19Q GAIN WILD-TYPE  321   24
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               68                321
  1                6                 24
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    26  53
  19Q GAIN WILD-TYPE 132 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     26   53
  19Q GAIN WILD-TYPE  132  230
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               26                132
  MALE                 53                230
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    53  18
  19Q GAIN WILD-TYPE 269  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     53   18
  19Q GAIN WILD-TYPE  269   58
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                53                269
  YES               18                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  19Q GAIN MUTATED                                          3
  19Q GAIN WILD-TYPE                                       10
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  19Q GAIN MUTATED                                      14
  19Q GAIN WILD-TYPE                                    58
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                       24
  19Q GAIN WILD-TYPE                                                    139
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  19Q GAIN MUTATED                                                   4
  19Q GAIN WILD-TYPE                                                17
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                                  16
  19Q GAIN WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  19Q GAIN MUTATED                                                    0
  19Q GAIN WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  19Q GAIN MUTATED                                                 16
  19Q GAIN WILD-TYPE                                               63
D35V9, multiclass
                                                                   clus
vv                                                                  19Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           14
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          24
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               16
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                16
                                                                   clus
vv                                                                  19Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             58
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  63
[1] 7 2
[1] TRUE
[1] "dimension of 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    56   6   6   4
  19Q GAIN WILD-TYPE 293  12  13  21
D35V10, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               56                293
  R1                6                 12
  R2                6                 13
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19Q GAIN MUTATED      18                         3
  19Q GAIN WILD-TYPE    70                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           1    45
  19Q GAIN WILD-TYPE                                         0   233
D35V12, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                                   18                 70
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   45                233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0  53
  19Q GAIN WILD-TYPE   5 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   53
  19Q GAIN WILD-TYPE    5  263
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               53                263
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   134  98
  20P GAIN WILD-TYPE 112  71
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               232                183 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                98                 71 
$`20P GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       47.05        79.07         0.23        20.15         9.86        27.35 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         4.08         9.67         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6706 
       13.87        13.68        19.33        39.12         9.17        18.05 
TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       19.89        40.21        21.90         9.21        35.24        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        28.73         3.45        29.56        33.21 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
       11.44         0.69         9.60         0.56        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 
       15.58         7.40        14.04        14.79         7.36         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8676 
       25.18         9.21        20.22        27.12         9.34         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       26.73        24.79         9.86        20.88         8.22        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 
       13.87         7.53        34.98         1.48         0.72         0.53 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
       13.51         0.46        20.42         1.15        21.44        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15        13.18        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
       12.33        12.30        12.39        11.64        15.39        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        12.30        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 
       11.77        20.02        27.02        15.95         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        4.01        14.01        12.03        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       30.97        36.00         1.02         0.99        12.03        28.96 
TCGA-CG-5730 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
        4.01         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 
       18.54        13.35        17.19        10.26        15.22        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8579 TCGA-D7-A4YT 
       11.31        12.33        24.72        19.50        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       16.44         5.92        36.43        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-8122 
       20.32        22.29        15.65         8.38        19.96         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23        11.38        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HJ-7597 TCGA-HU-8238 
       17.06         0.56         5.52         6.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        24.39        18.15        21.07         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.26         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI 
       23.84        21.17        33.40        36.36         3.45        18.38 
TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
       13.35         6.74        12.59        10.62        11.70        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        5.56        63.62        37.64        14.04        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
       74.53         6.08         9.24         8.61        16.67       122.30 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DV 
      115.69        57.44         8.94        35.61         5.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF 
       13.02        43.36        21.73        46.26        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       12.79         2.70        17.85        15.65        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       39.45        21.83        18.74        32.88         1.71        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A92D 
        9.73        55.56         9.04         2.01         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       21.04        42.54        11.24        18.41        38.93        32.94 
TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        12.43        17.26         0.79 

$`20P GAIN WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 
       21.99        22.98        16.24        26.93        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 
       11.70        19.56         7.43         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
        9.57        34.68        17.29        26.10        32.78        25.61 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7703 
       12.16         8.98        30.90        31.20        44.94        36.16 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
       35.84        39.78         9.07        37.25        14.43        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8360 TCGA-BR-8361 
       32.25         8.05        29.42         2.66         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 
        4.31         3.32        11.80        31.27        25.05         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-8682 
        1.12        12.79        28.14         6.28        31.96        32.58 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.13         6.08        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4QL 
       14.17        28.34         0.66        32.52        20.65        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8531 
        5.13        13.41        13.35        11.21        12.10        12.59 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 
       12.07        12.43        11.31        12.62         3.02         1.02 
TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 
        8.05        29.98        19.07         0.00         9.01         6.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5732 
        0.99         6.02       105.07        15.02        65.10        69.04 
TCGA-CG-5733 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 
       21.07        20.55        18.84        18.61        17.85        15.98 
TCGA-D7-6817 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.79        16.80        17.19        18.21        14.66        21.14 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       13.78        14.76        11.44         4.34         7.13         0.62 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 
       21.27         3.48        59.54         5.03        13.58        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       63.06        52.21        30.51        28.96        22.32        22.82 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT 
        5.59        22.68        24.20        21.37        29.98         6.51 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8462 TCGA-IN-8663 
       29.00        23.80        14.07        15.68        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IP-7968 
       12.46        19.53         6.44         6.51        15.75         2.53 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A804 TCGA-RD-A7BS 
       36.95         3.72        19.73        45.67         4.60        11.05 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB 
        5.13        37.91        40.64       116.38        71.38        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E7 
       19.04         0.92        48.79         5.46        18.48        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       38.14        37.22         7.73        30.97        34.29        16.31 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY 
        1.87         9.27        23.41        13.35        29.59        14.33 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A924 
       11.70        61.22        20.81        42.64         9.50        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D 
        4.54         6.58         2.66        43.66        28.41        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       54.12        16.14        27.55 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               0.1                0.0 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            122.30             116.38 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             13.51              17.13 
[1] "0.1 - 122.3 (13.5)" "0.0 - 116.4 (17.1)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         1        9       19       16        22        29
  20P GAIN WILD-TYPE       1        7       22       16        18        27
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           2         51         36         22       20
  20P GAIN WILD-TYPE         1         30         27         17       24
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  9                  7
  STAGE IB                 19                 22
  STAGE II                 16                 16
  STAGE IIA                22                 18
  STAGE IIB                29                 27
  STAGE III                 2                  1
  STAGE IIIA               51                 30
  STAGE IIIB               36                 27
  STAGE IIIC               22                 17
  STAGE IV                 20                 24
[1] 11  2
[1] 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    11  49 116  60
  20P GAIN WILD-TYPE  12  44  80  59
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               11                 12
  T2               49                 44
  T3              116                 80
  T4               60                 59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20P GAIN MUTATED   63 73 46 47
  20P GAIN WILD-TYPE 67 46 40 41
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               63                 67
  N1               73                 46
  N2               46                 40
  N3               47                 41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   217  13
  20P GAIN WILD-TYPE 172  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    217   13
  20P GAIN WILD-TYPE  172   17
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              217                172
  1               13                 17
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    76 166
  20P GAIN WILD-TYPE  82 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     76  166
  20P GAIN WILD-TYPE   82  117
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               76                 82
  MALE                166                117
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   184  34
  20P GAIN WILD-TYPE 138  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    184   34
  20P GAIN WILD-TYPE  138   42
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               184                138
  YES               34                 42
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  20P GAIN MUTATED                                          8
  20P GAIN WILD-TYPE                                        5
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  20P GAIN MUTATED                                      30
  20P GAIN WILD-TYPE                                    42
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                       84
  20P GAIN WILD-TYPE                                                     79
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  20P GAIN MUTATED                                                  10
  20P GAIN WILD-TYPE                                                11
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                                  53
  20P GAIN WILD-TYPE                                                                29
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  20P GAIN MUTATED                                                    5
  20P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  20P GAIN MUTATED                                                 51
  20P GAIN WILD-TYPE                                               28
D36V9, multiclass
                                                                   clus
vv                                                                  20P GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           30
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          84
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               53
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                51
                                                                   clus
vv                                                                  20P GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             42
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            79
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 29
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  28
[1] 7 2
[1] TRUE
[1] "dimension of 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   192   9   9  14
  20P GAIN WILD-TYPE 157   9  10  11
D36V10, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              192                157
  R1                9                  9
  R2                9                 10
  RX               14                 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"
D36V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20P GAIN MUTATED      53                         6
  20P GAIN WILD-TYPE    35                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           1   151
  20P GAIN WILD-TYPE                                         0   127
D36V12, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                                   53                 35
  BLACK OR AFRICAN AMERICAN                                6                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  151                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"
D36V13, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2 179
  20P GAIN WILD-TYPE   3 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  179
  20P GAIN WILD-TYPE    3  137
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              179                137
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   157 111
  20Q GAIN WILD-TYPE  89  58
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               268                147 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               111                 58 
$`20Q GAIN MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        27.35        58.03        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4255 
        6.61         6.97         4.64        18.35        30.90         4.08 
TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.67         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 
       19.33        39.12        26.10         9.17        18.05        19.89 
TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
       40.21        21.90         9.21        35.24        33.63        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       15.32        28.73         3.45        29.56        33.21        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
       11.44         0.69         9.60         0.56         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 
        2.20        15.58         7.40        14.04        14.79         7.36 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        27.12         9.34 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        8.22        10.68        13.87         7.53        34.98         1.48 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.89         0.72         0.53        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       20.42         1.15        21.44        13.02        13.15        13.18 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
       12.30        12.39        11.64        15.39        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        4.01        14.01        12.03        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       30.97        36.00         1.02         0.99        12.03        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       19.13        20.55        18.84        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        19.50        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27        16.44         5.92        36.43        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A 
       11.31        20.32        22.29        15.65         8.38        19.96 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       14.07        22.29        17.06         0.56         5.52         6.21 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       52.21        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       28.96        22.82        21.07         0.76        24.30        24.26 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
       23.80        21.17        33.40        36.36         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       18.38        13.35         6.74        12.59        10.62        11.70 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A666 
       13.51         2.53         5.56        63.62        37.64        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT 
       45.67        18.21         8.52        74.53         6.08         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
       16.67       122.30        37.91       115.69        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       35.61         5.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       43.36        21.73        46.26        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
        2.70        17.85        15.65        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       39.45        21.83        18.74        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        4.54         5.72        66.81        21.04        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

$`20Q GAIN WILD-TYPE`
TCGA-CG-4460 TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 
       21.99        26.93        26.70        11.70        19.56         7.43 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6566 
        4.08         9.34         6.18         9.57        34.68        32.78 
TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       25.61        12.16         8.98        30.90        31.20        44.94 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8078 
       36.16        35.84        39.78         9.07        37.25        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       32.25         8.05        29.42         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 
        3.32        11.80        31.27        25.05         3.72         1.12 
TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-A44T TCGA-BR-A453 
       12.79        28.14         6.28        31.96        34.13         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       27.55        28.57         8.98        14.17        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 
       32.52        16.14         5.13        13.41        13.35        11.21 
TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MJ TCGA-CG-4301 
       12.59        12.07        12.43        11.31        12.62         3.02 
TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 
        1.02        29.98        19.07         0.00         9.01         6.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5733 
        0.99         6.02       105.07        15.02        65.10        21.07 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-A4YY 
       18.61        17.85        12.79        17.19        18.21        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-A448 
       14.76        11.44         4.34         7.13         0.62        21.27 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
       59.54         5.03        13.58        77.29        63.06        30.51 
TCGA-HU-8602 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.32         5.59        22.68        24.20        21.37        29.98 
TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8462 TCGA-IN-A6RJ 
        6.51        29.00        14.07        15.68        18.81        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93J TCGA-MX-A5UG 
       19.53         6.44         6.51        15.75        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8N0 
       19.73         4.60         9.24        11.05         5.13        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT 
      116.38        71.38        16.87        19.04         0.92        48.79 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PT 
       16.31         1.87         9.27        23.41        13.35        29.59 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P 
       11.70        61.22        20.81        55.43         6.58         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6I 
       28.41        17.13        16.14 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               0.1                0.0 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            122.30             116.38 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             14.30              16.14 
[1] "0.1 - 122.3 (14.3)" "0.0 - 116.4 (16.1)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         1       10       24       17        24        38
  20Q GAIN WILD-TYPE       1        6       17       15        16        18
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           3         58         42         23       23
  20Q GAIN WILD-TYPE         0         23         21         16       21
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 10                  6
  STAGE IB                 24                 17
  STAGE II                 17                 15
  STAGE IIA                24                 16
  STAGE IIB                38                 18
  STAGE III                 3                  0
  STAGE IIIA               58                 23
  STAGE IIIB               42                 21
  STAGE IIIC               23                 16
  STAGE IV                 23                 21
[1] 11  2
[1] 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    12  61 133  68
  20Q GAIN WILD-TYPE  11  32  63  51
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               12                 11
  T2               61                 32
  T3              133                 63
  T4               68                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20Q GAIN MUTATED   74 82 60 51
  20Q GAIN WILD-TYPE 56 37 26 37
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               74                 56
  N1               82                 37
  N2               60                 26
  N3               51                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   248  15
  20Q GAIN WILD-TYPE 141  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    248   15
  20Q GAIN WILD-TYPE  141   15
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              248                141
  1               15                 15
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    86 194
  20Q GAIN WILD-TYPE  72  89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     86  194
  20Q GAIN WILD-TYPE   72   89
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               86                 72
  MALE                194                 89
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   211  44
  20Q GAIN WILD-TYPE 111  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    211   44
  20Q GAIN WILD-TYPE  111   32
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               211                111
  YES               44                 32
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  20Q GAIN MUTATED                                          8
  20Q GAIN WILD-TYPE                                        5
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  20Q GAIN MUTATED                                      32
  20Q GAIN WILD-TYPE                                    40
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                       96
  20Q GAIN WILD-TYPE                                                     67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  20Q GAIN MUTATED                                                  11
  20Q GAIN WILD-TYPE                                                10
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                                  62
  20Q GAIN WILD-TYPE                                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  20Q GAIN MUTATED                                                    6
  20Q GAIN WILD-TYPE                                                  2
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  20Q GAIN MUTATED                                                 62
  20Q GAIN WILD-TYPE                                               17
D37V9, multiclass
                                                                   clus
vv                                                                  20Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           32
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          96
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                62
                                                                   clus
vv                                                                  20Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             40
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            67
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  17
[1] 7 2
[1] TRUE
[1] "dimension of 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   228   9  10  14
  20Q GAIN WILD-TYPE 121   9   9  11
D37V10, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              228                121
  R1                9                  9
  R2               10                  9
  RX               14                 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"
D37V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20Q GAIN MUTATED      59                         9
  20Q GAIN WILD-TYPE    29                         3
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           1   174
  20Q GAIN WILD-TYPE                                         0   104
D37V12, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                                   59                 29
  BLACK OR AFRICAN AMERICAN                                9                  3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  174                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"
D37V13, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     4 201
  20Q GAIN WILD-TYPE   1 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4  201
  20Q GAIN WILD-TYPE    1  115
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO              201                115
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    11   9
  21Q GAIN WILD-TYPE 235 160
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                20                395 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 9                160 
$`21Q GAIN MUTATED`
TCGA-BR-6456 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8486 
       17.29         3.45         0.69        29.42         2.20        20.22 
TCGA-BR-8687 TCGA-BR-A44U TCGA-CD-5799 TCGA-CD-A486 TCGA-D7-6527 TCGA-D7-6528 
        8.22        13.87        13.02         6.31        10.26        15.22 
TCGA-D7-6822 TCGA-D7-A6F0 TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4HD 
       12.33        22.29         5.92        22.75        11.77        33.40 
TCGA-IN-A6RP TCGA-VQ-A8PC 
        6.44        46.26 

$`21Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 
       20.15         9.86        27.35        26.93        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43        11.44        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
       32.25         8.05         0.56         2.66        19.96        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86        20.88        10.68        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        1.15        21.44        16.14         5.13        13.41        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       11.64        15.39        12.07        12.82        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85        13.35        17.19        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       63.62        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       21.83        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.69               0.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             46.26             122.30 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            12.675             15.320 
[1] "0.7 - 46.3 (12.7)"  "0.0 - 122.3 (15.3)"
[1] "hr=" "1.4"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         0        2        3        3         2         4
  21Q GAIN WILD-TYPE       2       14       38       29        38        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           0          2          2          3        1
  21Q GAIN WILD-TYPE         3         79         61         36       43
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 14
  STAGE IB                  3                 38
  STAGE II                  3                 29
  STAGE IIA                 2                 38
  STAGE IIB                 4                 52
  STAGE III                 0                  3
  STAGE IIIA                2                 79
  STAGE IIIB                2                 61
  STAGE IIIC                3                 36
  STAGE IV                  1                 43
[1] 11  2
[1] 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     3   5   9   5
  21Q GAIN WILD-TYPE  20  88 187 114
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                 20
  T2                5                 88
  T3                9                187
  T4                5                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q GAIN MUTATED     9   7   3   3
  21Q GAIN WILD-TYPE 121 112  83  85
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                9                121
  N1                7                112
  N2                3                 83
  N3                3                 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"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    21   1
  21Q GAIN WILD-TYPE 368  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     21    1
  21Q GAIN WILD-TYPE  368   29
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               21                368
  1                1                 29
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     8  14
  21Q GAIN WILD-TYPE 150 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8   14
  21Q GAIN WILD-TYPE  150  269
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                8                150
  MALE                 14                269
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    17   2
  21Q GAIN WILD-TYPE 305  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     17    2
  21Q GAIN WILD-TYPE  305   74
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                17                305
  YES                2                 74
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  21Q GAIN MUTATED                                          1
  21Q GAIN WILD-TYPE                                       12
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  21Q GAIN MUTATED                                       1
  21Q GAIN WILD-TYPE                                    71
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                       10
  21Q GAIN WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  21Q GAIN MUTATED                                                   0
  21Q GAIN WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                                   3
  21Q GAIN WILD-TYPE                                                                79
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  21Q GAIN MUTATED                                                    1
  21Q GAIN WILD-TYPE                                                  7
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  21Q GAIN MUTATED                                                  6
  21Q GAIN WILD-TYPE                                               73
D38V9, multiclass
                                                                   clus
vv                                                                  21Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 6
                                                                   clus
vv                                                                  21Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             71
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 79
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  73
[1] 7 2
[1] TRUE
[1] "dimension of 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    18   1   1   0
  21Q GAIN WILD-TYPE 331  17  18  25
D38V10, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               18                331
  R1                1                 17
  R2                1                 18
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  21Q GAIN MUTATED       6                         0
  21Q GAIN WILD-TYPE    82                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           0    15
  21Q GAIN WILD-TYPE                                         1   263
D38V12, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                                    6                 82
  BLACK OR AFRICAN AMERICAN                                0                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  20
  21Q GAIN WILD-TYPE   5 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   20
  21Q GAIN WILD-TYPE    5  296
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               20                296
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    20  10
  22Q GAIN WILD-TYPE 226 159
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                30                385 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                10                159 
$`22Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8486 
       11.70         4.64        35.24        28.73        33.21        20.22 
TCGA-BR-A452 TCGA-BR-A4J8 TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8528 TCGA-CG-4436 
        7.53        13.51        13.02        12.59        12.33         7.99 
TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4Z0 TCGA-D7-A6F0 TCGA-F1-6875 
       18.54        15.98        14.66        14.76        22.29        72.23 
TCGA-FP-7998 TCGA-HU-8604 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-IN-7808 
       22.29        22.82        11.77         6.58        23.80         3.45 
TCGA-KB-A6F7 TCGA-RD-A8N6 TCGA-VQ-A8PJ TCGA-VQ-A91D TCGA-VQ-AA68 TCGA-VQ-AA6K 
       63.62         8.94         2.70        11.70        43.66        12.43 

$`22Q GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 
       20.15         9.86        27.35        26.93        58.03        26.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       15.32         3.45         9.07        29.56        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        1.15        21.44        16.14         5.13        13.41        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.84        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       14.07        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK 
       46.26        16.31        22.19         2.50        12.79        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        73.41        39.45        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.54        11.24        18.41        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       17.13        54.12        26.04        16.14        27.55        17.26 
TCGA-ZQ-A9CR 
        0.79 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               2.7                0.0 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             72.23             122.30 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            14.085             15.220 
[1] "2.7 - 72.2 (14.1)"  "0.0 - 122.3 (15.2)"
[1] "hr=" "1.3"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         0        4        5        2         2         3
  22Q GAIN WILD-TYPE       2       12       36       30        38        53
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           0          5          3          4        1
  22Q GAIN WILD-TYPE         3         76         60         35       43
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  4                 12
  STAGE IB                  5                 36
  STAGE II                  2                 30
  STAGE IIA                 2                 38
  STAGE IIB                 3                 53
  STAGE III                 0                  3
  STAGE IIIA                5                 76
  STAGE IIIB                3                 60
  STAGE IIIC                4                 35
  STAGE IV                  1                 43
[1] 11  2
[1] 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     4  10   9   8
  22Q GAIN WILD-TYPE  19  83 187 111
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                4                 19
  T2               10                 83
  T3                9                187
  T4                8                111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q GAIN MUTATED    12   6   6   7
  22Q GAIN WILD-TYPE 118 113  80  81
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               12                118
  N1                6                113
  N2                6                 80
  N3                7                 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"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    29   2
  22Q GAIN WILD-TYPE 360  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     29    2
  22Q GAIN WILD-TYPE  360   28
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               29                360
  1                2                 28
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    13  19
  22Q GAIN WILD-TYPE 145 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     13   19
  22Q GAIN WILD-TYPE  145  264
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               13                145
  MALE                 19                264
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    24   7
  22Q GAIN WILD-TYPE 298  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     24    7
  22Q GAIN WILD-TYPE  298   69
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                24                298
  YES                7                 69
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  22Q GAIN MUTATED                                          1
  22Q GAIN WILD-TYPE                                       12
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  22Q GAIN MUTATED                                       5
  22Q GAIN WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                        8
  22Q GAIN WILD-TYPE                                                    155
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  22Q GAIN MUTATED                                                   3
  22Q GAIN WILD-TYPE                                                18
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                                   7
  22Q GAIN WILD-TYPE                                                                75
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  22Q GAIN MUTATED                                                    1
  22Q GAIN WILD-TYPE                                                  7
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  22Q GAIN MUTATED                                                  7
  22Q GAIN WILD-TYPE                                               72
D39V9, multiclass
                                                                   clus
vv                                                                  22Q GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 7
                                                                   clus
vv                                                                  22Q GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 75
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  72
[1] 7 2
[1] TRUE
[1] "dimension of 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    27   1   1   1
  22Q GAIN WILD-TYPE 322  17  18  24
D39V10, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               27                322
  R1                1                 17
  R2                1                 18
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  22Q GAIN MUTATED       9                         1
  22Q GAIN WILD-TYPE    79                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    19
  22Q GAIN WILD-TYPE                                         1   259
D39V12, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                                    9                 79
  BLACK OR AFRICAN AMERICAN                                1                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   19                259
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  25
  22Q GAIN WILD-TYPE   4 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   25
  22Q GAIN WILD-TYPE    4  291
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               25                291
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    25  23
  XP GAIN WILD-TYPE 221 146
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               48               367 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               23               146 
$`XP GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-BR-4187 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7717 
       21.99        79.07         4.64        40.21         9.21        18.15 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8365 TCGA-BR-8678 TCGA-BR-8680 
       37.25        14.43         0.69        17.52        24.79        31.96 
TCGA-BR-A452 TCGA-BR-A4CS TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CG-4436 
        7.53         1.48        12.33        12.30         6.58         7.99 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5726 TCGA-D7-6519 TCGA-D7-8576 TCGA-D7-A6EV 
       12.00        36.00        28.96        20.55        14.66        11.24 
TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-HF-7133 
       22.29         0.62         7.99        72.23         3.48        63.06 
TCGA-HF-7134 TCGA-HU-8244 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GF 
       52.21        24.39        24.30        24.26        24.20        25.81 
TCGA-HU-A4GT TCGA-HU-A4HD TCGA-IN-7808 TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-RD-A8N6 
        6.51        33.40         3.45        18.21         8.61         8.94 
TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91U 
       48.79        18.48        14.33        21.83        20.81         1.71 

$`XP GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       27.35        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         6.97         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        44.94        21.90        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.84        33.63        39.78        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
        9.07        29.56        33.21        11.44        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       26.73        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       34.13        13.87         6.08        34.98        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        20.91        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.31        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        4.34        19.96         7.13        14.47        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-A5NB 
       13.58         0.56         5.52         6.21        77.29        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC 
       22.82        21.07         0.76         5.59        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        23.80        21.17        14.07        15.68        36.36 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       15.75        13.51         2.53         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       36.95         3.72        19.73        14.04        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       74.53         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92         5.46        13.25        13.02        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       29.59        64.57        73.41        39.45        11.70        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        32.88        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        5.72        66.81        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.62              0.00 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            79.07            122.30 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            18.18             14.47 
[1] "0.6 - 79.1 (18.2)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         0        6        5        3         5         4
  XP GAIN WILD-TYPE       2       10       36       29        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED           1          7          6          1        9
  XP GAIN WILD-TYPE         2         74         57         38       35
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 6                10
  STAGE IB                 5                36
  STAGE II                 3                29
  STAGE IIA                5                35
  STAGE IIB                4                52
  STAGE III                1                 2
  STAGE IIIA               7                74
  STAGE IIIB               6                57
  STAGE IIIC               1                38
  STAGE IV                 9                35
[1] 11  2
[1] 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     5  12  20  13
  XP GAIN WILD-TYPE  18  81 176 106
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               5                18
  T2              12                81
  T3              20               176
  T4              13               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XP GAIN MUTATED    20  12   9   8
  XP GAIN WILD-TYPE 110 107  77  80
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              20               110
  N1              12               107
  N2               9                77
  N3               8                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    45   4
  XP GAIN WILD-TYPE 344  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     45    4
  XP GAIN WILD-TYPE  344   26
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              45               344
  1               4                26
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    23  28
  XP GAIN WILD-TYPE 135 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     23   28
  XP GAIN WILD-TYPE  135  255
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              23               135
  MALE                28               255
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    38   9
  XP GAIN WILD-TYPE 284  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     38    9
  XP GAIN WILD-TYPE  284   67
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               38               284
  YES               9                67
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  XP GAIN MUTATED                                          0
  XP GAIN WILD-TYPE                                       13
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  XP GAIN MUTATED                                       5
  XP GAIN WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XP GAIN MUTATED                                                       16
  XP GAIN WILD-TYPE                                                    147
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  XP GAIN MUTATED                                                   1
  XP GAIN WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XP GAIN MUTATED                                                                  15
  XP GAIN WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  XP GAIN MUTATED                                                    1
  XP GAIN WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  XP GAIN MUTATED                                                 12
  XP GAIN WILD-TYPE                                               67
D40V9, multiclass
                                                                   clus
vv                                                                  XP GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              15
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               12
                                                                   clus
vv                                                                  XP GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         13
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 67
[1] 7 2
[1] TRUE
[1] "dimension of 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    40   1   3   3
  XP GAIN WILD-TYPE 309  17  16  22
D40V10, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              40               309
  R1               1                17
  R2               3                16
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XP GAIN MUTATED      13                         3
  XP GAIN WILD-TYPE    75                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP GAIN MUTATED                                           1    24
  XP GAIN WILD-TYPE                                         0   254
D40V12, multiclass
                                           clus
vv                                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                                  13                75
  BLACK OR AFRICAN AMERICAN                               3                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  24               254
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0  37
  XP GAIN WILD-TYPE   5 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   37
  XP GAIN WILD-TYPE    5  279
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              37               279
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    29  22
  XQ GAIN WILD-TYPE 217 147
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               51               364 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               22               147 
$`XQ GAIN MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-BR-4187 TCGA-BR-6801 TCGA-BR-7717 TCGA-BR-8058 
       21.99        79.07         4.64        40.21        18.15        37.25 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8680 TCGA-BR-8683 
       14.43         0.69        13.08        17.52        31.96         9.86 
TCGA-BR-A452 TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CG-4472 TCGA-CG-5718 
        7.53        12.33        12.30         6.58        12.00        36.00 
TCGA-CG-5726 TCGA-CG-5734 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-A6EV 
       28.96         7.99        17.19        15.22        15.98        11.24 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 
       22.29        15.65         0.62         7.99        72.23         3.48 
TCGA-HF-7134 TCGA-HU-8244 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD 
       52.21        24.39        24.30        24.26        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4HD TCGA-IN-7808 TCGA-R5-A7O7 TCGA-RD-A7BT 
       25.81         6.51        33.40         3.45        45.67         8.61 
TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8PC TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91U 
        8.94        48.79        46.26        14.33        21.83         1.71 
TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-AA68 
       55.56        66.81        43.66 

$`XQ GAIN WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       27.35        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         6.97         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        33.63        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8078 
        3.45         9.07        29.56        33.21        11.44        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       26.73        24.79        32.58        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        6.31        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        13.35        10.26 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.31        11.44        20.32         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
       19.96         7.13        14.47        21.27        11.38        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
        0.56         5.52         6.21        77.29        63.06        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC 
       22.82        21.07         0.76         5.59        22.68         3.25 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       23.80        21.17        14.07        15.68        36.36        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N 
       64.57        73.41        39.45        11.70        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       20.81        32.88        42.64        60.85         9.50         9.73 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
       21.04         2.66        42.54        11.24        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       38.93        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.62              0.00 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            79.07            122.30 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            17.52             14.22 
[1] "0.6 - 79.1 (17.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         0        6        6        2         5         6
  XQ GAIN WILD-TYPE       2       10       35       30        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           1          9          7          2        8
  XQ GAIN WILD-TYPE         2         72         56         37       36
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 6                10
  STAGE IB                 6                35
  STAGE II                 2                30
  STAGE IIA                5                35
  STAGE IIB                6                50
  STAGE III                1                 2
  STAGE IIIA               9                72
  STAGE IIIB               7                56
  STAGE IIIC               2                37
  STAGE IV                 8                36
[1] 11  2
[1] 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     5  12  22  15
  XQ GAIN WILD-TYPE  18  81 174 104
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               5                18
  T2              12                81
  T3              22               174
  T4              15               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"
                   vv
clus                 N0  N1  N2  N3
  XQ GAIN MUTATED    20  16  11   6
  XQ GAIN WILD-TYPE 110 103  75  82
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              20               110
  N1              16               103
  N2              11                75
  N3               6                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    47   5
  XQ GAIN WILD-TYPE 342  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     47    5
  XQ GAIN WILD-TYPE  342   25
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              47               342
  1               5                25
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    24  31
  XQ GAIN WILD-TYPE 134 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     24   31
  XQ GAIN WILD-TYPE  134  252
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              24               134
  MALE                31               252
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    43   7
  XQ GAIN WILD-TYPE 279  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     43    7
  XQ GAIN WILD-TYPE  279   69
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               43               279
  YES               7                69
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  XQ GAIN MUTATED                                          1
  XQ GAIN WILD-TYPE                                       12
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  XQ GAIN MUTATED                                       4
  XQ GAIN WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                       15
  XQ GAIN WILD-TYPE                                                    148
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  XQ GAIN MUTATED                                                   0
  XQ GAIN WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                                  14
  XQ GAIN WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  XQ GAIN MUTATED                                                    1
  XQ GAIN WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  XQ GAIN MUTATED                                                 19
  XQ GAIN WILD-TYPE                                               60
D41V9, multiclass
                                                                   clus
vv                                                                  XQ GAIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              14
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               19
                                                                   clus
vv                                                                  XQ GAIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of 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    44   0   3   3
  XQ GAIN WILD-TYPE 305  18  16  22
D41V10, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              44               305
  R1               0                18
  R2               3                16
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XQ GAIN MUTATED      15                         2
  XQ GAIN WILD-TYPE    73                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           1    29
  XQ GAIN WILD-TYPE                                         0   249
D41V12, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                                  15                73
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  29               249
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  39
  XQ GAIN WILD-TYPE   4 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   39
  XQ GAIN WILD-TYPE    4  277
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              39               277
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    30  27
  1P LOSS WILD-TYPE 216 142
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               57               358 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               27               142 
$`1P LOSS MUTATED`
TCGA-EQ-A4SO TCGA-MX-A663 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 
       16.24         9.86        11.01         9.44         6.61        17.29 
TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8485 TCGA-BR-8678 
       19.33        35.24        33.21         2.66         9.21        24.79 
TCGA-BR-8683 TCGA-BR-A452 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
        9.86         7.53        20.42         1.15        21.44        13.02 
TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 
       13.35         7.17        15.39         6.31        11.31        20.02 
TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 
        3.02        54.08         1.02        12.03         4.01        20.91 
TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8573 TCGA-EQ-5647 
       20.55        17.19        10.26        15.22        19.50         0.62 
TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GP TCGA-HU-A4HD TCGA-KB-A93H 
        5.52        28.96        22.82         8.98        33.40        37.64 
TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PE 
       18.21         8.61        13.25        13.02         7.73        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A91A TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O 
        2.70        39.45        55.56         4.54        66.81        21.04 
TCGA-VQ-AA6B TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       32.94        12.43         0.79 

$`1P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       27.35        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56        29.42        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL 
        0.66        32.52        13.51         0.46        20.65        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 
        5.13        13.41        13.15        13.18        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       12.59        11.64        12.07        12.82        12.43        12.30 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02         7.99         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
       15.65         8.38         4.34        19.96         7.13         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        18.15        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       37.22        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       13.35        29.59        64.57        14.33        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       21.83        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 
       42.64        60.85         9.50         9.73         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
       55.43         6.58         5.72         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        16.14        27.55        17.26 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.62              0.00 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            66.81            122.30 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            13.25             15.17 
[1] "0.6 - 66.8 (13.2)"  "0.0 - 122.3 (15.2)"
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         0        0        5        6         8         5
  1P LOSS WILD-TYPE       2       16       36       26        32        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           0         11          7          4       10
  1P LOSS WILD-TYPE         3         70         56         35       34
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                16
  STAGE IB                 5                36
  STAGE II                 6                26
  STAGE IIA                8                32
  STAGE IIB                5                51
  STAGE III                0                 3
  STAGE IIIA              11                70
  STAGE IIIB               7                56
  STAGE IIIC               4                35
  STAGE IV                10                34
[1] 11  2
[1] 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     0  12  28  18
  1P LOSS WILD-TYPE  23  81 168 101
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               0                23
  T2              12                81
  T3              28               168
  T4              18               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P LOSS MUTATED    16  15  13  11
  1P LOSS WILD-TYPE 114 104  73  77
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              16               114
  N1              15               104
  N2              13                73
  N3              11                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    48   8
  1P LOSS WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     48    8
  1P LOSS WILD-TYPE  341   22
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              48               341
  1               8                22
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    21  37
  1P LOSS WILD-TYPE 137 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     21   37
  1P LOSS WILD-TYPE  137  246
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              21               137
  MALE                37               246
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    44   8
  1P LOSS WILD-TYPE 278  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     44    8
  1P LOSS WILD-TYPE  278   68
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               44               278
  YES               8                68
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  1P LOSS MUTATED                                          3
  1P LOSS WILD-TYPE                                       10
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  1P LOSS MUTATED                                       4
  1P LOSS WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                       16
  1P LOSS WILD-TYPE                                                    147
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  1P LOSS MUTATED                                                   3
  1P LOSS WILD-TYPE                                                18
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                                  13
  1P LOSS WILD-TYPE                                                                69
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  1P LOSS MUTATED                                                    1
  1P LOSS WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  1P LOSS MUTATED                                                 17
  1P LOSS WILD-TYPE                                               62
D42V9, multiclass
                                                                   clus
vv                                                                  1P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              13
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               17
                                                                   clus
vv                                                                  1P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                69
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 62
[1] 7 2
[1] TRUE
[1] "dimension of 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    38   3   8   2
  1P LOSS WILD-TYPE 311  15  11  23
D42V10, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              38               311
  R1               3                15
  R2               8                11
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1P LOSS MUTATED      13                         2
  1P LOSS WILD-TYPE    75                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           1    35
  1P LOSS WILD-TYPE                                         0   243
D42V12, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                                  13                75
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  35               243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  39
  1P LOSS WILD-TYPE   5 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   39
  1P LOSS WILD-TYPE    5  277
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              39               277
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    13  12
  1Q LOSS WILD-TYPE 233 157
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               390 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               157 
$`1Q LOSS MUTATED`
TCGA-EQ-A4SO TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7704 
       16.24         9.44         6.61        17.29        19.33        35.24 
TCGA-BR-8289 TCGA-CD-5799 TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-5724 TCGA-CG-5730 
        2.66        13.02         6.31        12.43        12.03         4.01 
TCGA-D7-6519 TCGA-HU-8604 TCGA-HU-A4GP TCGA-HU-A4HD TCGA-IN-8663 TCGA-IP-7968 
       20.55        22.82         8.98        33.40         3.39         2.53 
TCGA-KB-A93H TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PE TCGA-VQ-A925 TCGA-VQ-AA6B 
       37.64        13.25        13.02        22.19         4.54        32.94 
TCGA-ZQ-A9CR 
        0.79 

$`1Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        9.86        27.35        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       19.56        11.01         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79         5.46        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        55.56         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       11.24        18.41        43.66        28.41        38.93        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.79              0.00 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            37.64            122.30 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            13.02             15.27 
[1] "0.8 - 37.6 (13.0)"  "0.0 - 122.3 (15.3)"
[1] "hr=" "1.5"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         0        0        1        2         4         5
  1Q LOSS WILD-TYPE       2       16       40       30        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           0          3          4          1        4
  1Q LOSS WILD-TYPE         3         78         59         38       40
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                16
  STAGE IB                 1                40
  STAGE II                 2                30
  STAGE IIA                4                36
  STAGE IIB                5                51
  STAGE III                0                 3
  STAGE IIIA               3                78
  STAGE IIIB               4                59
  STAGE IIIC               1                38
  STAGE IV                 4                40
[1] 11  2
[1] 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     0   6  14   5
  1Q LOSS WILD-TYPE  23  87 182 114
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               0                23
  T2               6                87
  T3              14               182
  T4               5               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q LOSS MUTATED     5   9   5   5
  1Q LOSS WILD-TYPE 125 110  81  83
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               5               125
  N1               9               110
  N2               5                81
  N3               5                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    18   4
  1Q LOSS WILD-TYPE 371  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     18    4
  1Q LOSS WILD-TYPE  371   26
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              18               371
  1               4                26
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    10  15
  1Q LOSS WILD-TYPE 148 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     10   15
  1Q LOSS WILD-TYPE  148  268
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              10               148
  MALE                15               268
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    19   4
  1Q LOSS WILD-TYPE 303  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     19    4
  1Q LOSS WILD-TYPE  303   72
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               19               303
  YES               4                72
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  1Q LOSS MUTATED                                          1
  1Q LOSS WILD-TYPE                                       12
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  1Q LOSS MUTATED                                       3
  1Q LOSS WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                        8
  1Q LOSS WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  1Q LOSS MUTATED                                                   0
  1Q LOSS WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                                   6
  1Q LOSS WILD-TYPE                                                                76
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  1Q LOSS MUTATED                                                    0
  1Q LOSS WILD-TYPE                                                  8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  1Q LOSS MUTATED                                                  6
  1Q LOSS WILD-TYPE                                               73
D43V9, multiclass
                                                                   clus
vv                                                                  1Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                6
                                                                   clus
vv                                                                  1Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                76
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 73
[1] 7 2
[1] TRUE
[1] "dimension of 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    16   0   4   1
  1Q LOSS WILD-TYPE 333  18  15  24
D43V10, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              16               333
  R1               0                18
  R2               4                15
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1Q LOSS MUTATED       7                         1
  1Q LOSS WILD-TYPE    81                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0    15
  1Q LOSS WILD-TYPE                                         1   263
D43V12, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                                   7                81
  BLACK OR AFRICAN AMERICAN                               1                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  15               263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  17
  1Q LOSS WILD-TYPE   5 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   17
  1Q LOSS WILD-TYPE    5  299
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              17               299
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    11  10
  2P LOSS WILD-TYPE 235 159
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               21               394 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               159 
$`2P LOSS MUTATED`
TCGA-CG-4475 TCGA-VQ-A8PU TCGA-BR-6565 TCGA-BR-8060 TCGA-BR-8687 TCGA-CD-8534 
       22.98        27.35         9.17        11.44         8.22        12.07 
TCGA-CD-8535 TCGA-CD-A48A TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 
       12.82        12.43        12.66        20.91        17.19        15.22 
TCGA-D7-8576 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-RD-A7C1 TCGA-RD-A8N9 
       14.66        63.06        26.47         5.92        16.67        35.61 
TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A91Z 
        5.46        18.48        55.56 

$`2P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.86        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        12.30        11.31        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        7.99        25.71        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85        13.35        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        5.52         6.21        77.29        52.21        30.51         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        48.79        13.25        13.02        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       21.83        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 
       42.64        60.85         9.50         9.73         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       38.93        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             5.46              0.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            63.06            122.30 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           15.220            14.775 
[1] "5.5 - 63.1 (15.2)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.1"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        0        4        2         1         3
  2P LOSS WILD-TYPE       2       16       37       30        39        53
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           0          8          1          3        1
  2P LOSS WILD-TYPE         3         73         62         36       43
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                16
  STAGE IB                 4                37
  STAGE II                 2                30
  STAGE IIA                1                39
  STAGE IIB                3                53
  STAGE III                0                 3
  STAGE IIIA               8                73
  STAGE IIIB               1                62
  STAGE IIIC               3                36
  STAGE IV                 1                43
[1] 11  2
[1] 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     0   7  11   5
  2P LOSS WILD-TYPE  23  86 185 114
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                23
  T2               7                86
  T3              11               185
  T4               5               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P LOSS MUTATED     7   5   7   4
  2P LOSS WILD-TYPE 123 114  79  84
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               7               123
  N1               5               114
  N2               7                79
  N3               4                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    21   0
  2P LOSS WILD-TYPE 368  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     21    0
  2P LOSS WILD-TYPE  368   30
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              21               368
  1               0                30
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    12  11
  2P LOSS WILD-TYPE 146 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     12   11
  2P LOSS WILD-TYPE  146  272
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              12               146
  MALE                11               272
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    17   6
  2P LOSS WILD-TYPE 305  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     17    6
  2P LOSS WILD-TYPE  305   70
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               17               305
  YES               6                70
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  2P LOSS MUTATED                                          1
  2P LOSS WILD-TYPE                                       12
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  2P LOSS MUTATED                                       3
  2P LOSS WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                        7
  2P LOSS WILD-TYPE                                                    156
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  2P LOSS MUTATED                                                   2
  2P LOSS WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                                   1
  2P LOSS WILD-TYPE                                                                81
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  2P LOSS MUTATED                                                    0
  2P LOSS WILD-TYPE                                                  8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  2P LOSS MUTATED                                                  8
  2P LOSS WILD-TYPE                                               71
D44V9, multiclass
                                                                   clus
vv                                                                  2P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                8
                                                                   clus
vv                                                                  2P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                81
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 71
[1] 7 2
[1] TRUE
[1] "dimension of 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    19   3   0   0
  2P LOSS WILD-TYPE 330  15  19  25
D44V10, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              19               330
  R1               3                15
  R2               0                19
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED       5                         1
  2P LOSS WILD-TYPE    83                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           0    14
  2P LOSS WILD-TYPE                                         1   264
D44V12, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                                   5                83
  BLACK OR AFRICAN AMERICAN                               1                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  14               264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  16
  2P LOSS WILD-TYPE   5 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   16
  2P LOSS WILD-TYPE    5  300
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              16               300
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    15  12
  2Q LOSS WILD-TYPE 231 157
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               27               388 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               12               157 
$`2Q LOSS MUTATED`
TCGA-CG-4475 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-BR-6565 TCGA-BR-8687 TCGA-CD-8534 
       22.98        27.35        26.93         9.17         8.22        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4300 TCGA-D7-5578 TCGA-D7-5579 
       12.82         6.31        12.43        20.02        12.66        20.91 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 
       17.19        15.22        14.66        63.06        26.47         5.92 
TCGA-HU-A4GD TCGA-HU-A4HD TCGA-IN-AB1V TCGA-R5-A7ZE TCGA-RD-A8N9 TCGA-VQ-A8DU 
       22.75        33.40        15.75        18.21        35.61         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-AA68 
       13.02        18.48        43.66 

$`2Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        9.86        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       17.29        13.68        19.33        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.43        12.30        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        10.26        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       77.29        52.21        30.51         1.51        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        24.26        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        23.80        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       11.70        13.51         2.53         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       36.95         3.72        19.73        14.04        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.79         0.92        48.79        13.25        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       21.83        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
       21.04         2.66        42.54        11.24        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       38.93        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             5.46              0.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            63.06            122.30 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            17.19             14.45 
[1] "5.5 - 63.1 (17.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         0        2        3        2         2         4
  2Q LOSS WILD-TYPE       2       14       38       30        38        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           0          9          2          4        2
  2Q LOSS WILD-TYPE         3         72         61         35       42
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                14
  STAGE IB                 3                38
  STAGE II                 2                30
  STAGE IIA                2                38
  STAGE IIB                4                52
  STAGE III                0                 3
  STAGE IIIA               9                72
  STAGE IIIB               2                61
  STAGE IIIC               4                35
  STAGE IV                 2                42
[1] 11  2
[1] 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     2   5  15   8
  2Q LOSS WILD-TYPE  21  88 181 111
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               2                21
  T2               5                88
  T3              15               181
  T4               8               111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q LOSS MUTATED    10   5   9   6
  2Q LOSS WILD-TYPE 120 114  77  82
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              10               120
  N1               5               114
  N2               9                77
  N3               6                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    27   1
  2Q LOSS WILD-TYPE 362  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     27    1
  2Q LOSS WILD-TYPE  362   29
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              27               362
  1               1                29
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    11  19
  2Q LOSS WILD-TYPE 147 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11   19
  2Q LOSS WILD-TYPE  147  264
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              11               147
  MALE                19               264
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    19   9
  2Q LOSS WILD-TYPE 303  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     19    9
  2Q LOSS WILD-TYPE  303   67
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               19               303
  YES               9                67
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  2Q LOSS MUTATED                                          3
  2Q LOSS WILD-TYPE                                       10
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  2Q LOSS MUTATED                                       3
  2Q LOSS WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                        9
  2Q LOSS WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  2Q LOSS MUTATED                                                   2
  2Q LOSS WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                                   1
  2Q LOSS WILD-TYPE                                                                81
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  2Q LOSS MUTATED                                                    0
  2Q LOSS WILD-TYPE                                                  8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  2Q LOSS MUTATED                                                 11
  2Q LOSS WILD-TYPE                                               68
D45V9, multiclass
                                                                   clus
vv                                                                  2Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               11
                                                                   clus
vv                                                                  2Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                81
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 68
[1] 7 2
[1] TRUE
[1] "dimension of 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    23   3   1   0
  2Q LOSS WILD-TYPE 326  15  18  25
D45V10, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              23               326
  R1               3                15
  R2               1                18
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2Q LOSS MUTATED       9                         2
  2Q LOSS WILD-TYPE    79                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           0    14
  2Q LOSS WILD-TYPE                                         1   264
D45V12, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                                   9                79
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  14               264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  19
  2Q LOSS WILD-TYPE   5 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   19
  2Q LOSS WILD-TYPE    5  297
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              19               297
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    53  37
  3P LOSS WILD-TYPE 193 132
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               90               325 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               37               132 
$`3P LOSS MUTATED`
TCGA-MX-A663 TCGA-VQ-A94U TCGA-B7-A5TJ TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6458 
        9.86        26.93        11.01         4.08        17.29        19.33 
TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7957 TCGA-BR-7959 
       31.20        35.24        33.63        39.78         9.07        33.21 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       37.25         0.69         2.66         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       20.22        20.88         8.22         7.53        34.98         1.48 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF 
       12.89         0.72         0.53        13.51        20.42         1.15 
TCGA-BR-A4QI TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A48A TCGA-CG-4300 TCGA-CG-4436 
       21.44         7.17        15.39        12.43        20.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5725 
        8.05        54.08         4.01        12.03        18.97        15.02 
TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
        4.01        12.66        18.54        13.35        17.19        15.22 
TCGA-D7-A6EX TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 
       11.31         0.62         7.99        19.53        14.07        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GC 
        0.56         5.52         6.21        18.15        28.96         3.25 
TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-IN-7806 TCGA-IN-A6RP TCGA-IN-A6RS 
       22.75         6.58        23.84        36.36         6.44        12.59 
TCGA-IN-A7NR TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A7ZE 
        6.51         5.56        37.64        36.95        45.67        18.21 
TCGA-R5-A7ZF TCGA-RD-A7C1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E0 
        8.52        16.67         8.94         5.79        13.25        18.48 
TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PY TCGA-VQ-A91X TCGA-VQ-A925 
       37.41        22.19         2.70        14.33         9.50         4.54 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       42.54        18.41        38.93        32.94        12.43         0.79 

$`3P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       20.15        27.35        58.03        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        30.90        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       21.90         9.21        36.16        35.84        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       28.73         3.45        29.56        14.43        11.44        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        9.60        32.25         8.05         0.56        29.42        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.05         3.72         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       32.58         9.86        10.68        34.13        13.87         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       27.55        28.57         8.98        14.17        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       32.52         0.46        20.65        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 
       12.62         3.02        27.02        15.95         1.02        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       29.98        19.07         0.00         9.01         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
        0.99       105.07        12.03        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.84        18.61        17.85        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        4.34        19.96         7.13        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       11.38         3.48        22.29        59.54         5.03        13.58 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF 
       24.30         5.59        24.26        22.68        24.20        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        33.40         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.39        18.38        12.46        13.35        19.53         6.74 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
       10.62        11.70        15.75        13.51         2.53        63.62 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        3.72        19.73        14.04        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       16.87        19.04         0.92        48.79         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       43.36        21.73        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK 
       34.29        46.26        16.31         2.50        12.79        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.73        55.56         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA68 
        5.72        66.81        21.04         2.66        11.24        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        17.13        54.12        26.04        16.14        27.55 
TCGA-ZA-A8F6 
       17.26 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.53              0.00 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            54.08            122.30 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            13.43             15.65 
[1] "0.5 - 54.1 (13.4)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1.2"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         0        3        8        6         7        13
  3P LOSS WILD-TYPE       2       13       33       26        33        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           0         20         13          8       11
  3P LOSS WILD-TYPE         3         61         50         31       33
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                13
  STAGE IB                 8                33
  STAGE II                 6                26
  STAGE IIA                7                33
  STAGE IIB               13                43
  STAGE III                0                 3
  STAGE IIIA              20                61
  STAGE IIIB              13                50
  STAGE IIIC               8                31
  STAGE IV                11                33
[1] 11  2
[1] 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     5  17  43  27
  3P LOSS WILD-TYPE  18  76 153  92
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               5                18
  T2              17                76
  T3              43               153
  T4              27                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P LOSS MUTATED    22  26  29  14
  3P LOSS WILD-TYPE 108  93  57  74
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              22               108
  N1              26                93
  N2              29                57
  N3              14                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    77  10
  3P LOSS WILD-TYPE 312  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     77   10
  3P LOSS WILD-TYPE  312   20
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              77               312
  1              10                20
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    33  60
  3P LOSS WILD-TYPE 125 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     33   60
  3P LOSS WILD-TYPE  125  223
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              33               125
  MALE                60               223
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    68  16
  3P LOSS WILD-TYPE 254  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     68   16
  3P LOSS WILD-TYPE  254   60
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               68               254
  YES              16                60
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  3P LOSS MUTATED                                          3
  3P LOSS WILD-TYPE                                       10
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  3P LOSS MUTATED                                       9
  3P LOSS WILD-TYPE                                    63
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                       33
  3P LOSS WILD-TYPE                                                    130
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  3P LOSS MUTATED                                                   4
  3P LOSS WILD-TYPE                                                17
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                                  24
  3P LOSS WILD-TYPE                                                                58
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  3P LOSS MUTATED                                                    1
  3P LOSS WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  3P LOSS MUTATED                                                 19
  3P LOSS WILD-TYPE                                               60
D46V9, multiclass
                                                                   clus
vv                                                                  3P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         33
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              24
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               19
                                                                   clus
vv                                                                  3P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                58
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of 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    76   3   5   2
  3P LOSS WILD-TYPE 273  15  14  23
D46V10, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              76               273
  R1               3                15
  R2               5                14
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED      17                         2
  3P LOSS WILD-TYPE    71                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           0    62
  3P LOSS WILD-TYPE                                         1   216
D46V12, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                                  17                71
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  62               216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  65
  3P LOSS WILD-TYPE   4 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   65
  3P LOSS WILD-TYPE    4  251
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              65               251
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    33  20
  3Q LOSS WILD-TYPE 213 149
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               53               362 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               20               149 
$`3Q LOSS MUTATED`
TCGA-MX-A663 TCGA-VQ-A94U TCGA-B7-A5TJ TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-7704 
        9.86        26.93        11.01         4.08        17.29        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8483 
       33.63        39.78        33.21         0.69         2.66         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4IY 
        9.21        20.22         8.22         7.53        34.98        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-A48A TCGA-CG-4438 
        0.72        13.51         1.15        21.44        12.43        54.08 
TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-A6EX 
        4.01        18.97        15.02        12.66        17.19        11.31 
TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GC 
        0.62        19.53        17.06         5.52        28.96         3.25 
TCGA-HU-A4GU TCGA-IN-7806 TCGA-IN-A6RS TCGA-IN-A7NR TCGA-KB-A6F5 TCGA-KB-A93H 
        6.58        36.36        12.59         6.51         5.56        37.64 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8PE 
       45.67        18.21         8.52        13.25        37.41        22.19 
TCGA-VQ-A8PY TCGA-VQ-A91X TCGA-VQ-A94R TCGA-VQ-AA6B TCGA-VQ-AA6K 
       14.33         9.50        42.54        32.94        12.43 

$`3Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       20.15        27.35        58.03        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
        9.86        20.88        10.68        34.13        13.87         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        1.48        27.55        28.57         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52         0.46        20.65        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        8.05        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         0.56         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
       19.53         6.44         6.74        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       14.04        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        18.48        43.36        21.73        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        29.59        64.57        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71        42.64        60.85         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       21.04         2.66        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        17.13        54.12        26.04        16.14        27.55 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.62              0.00 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            54.08            122.30 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           13.250            15.355 
[1] "0.6 - 54.1 (13.2)"  "0.0 - 122.3 (15.4)"
[1] "hr=" "1"  
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         0        3        3        1         5         9
  3Q LOSS WILD-TYPE       2       13       38       31        35        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           0         13          8          4        8
  3Q LOSS WILD-TYPE         3         68         55         35       36
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                13
  STAGE IB                 3                38
  STAGE II                 1                31
  STAGE IIA                5                35
  STAGE IIB                9                47
  STAGE III                0                 3
  STAGE IIIA              13                68
  STAGE IIIB               8                55
  STAGE IIIC               4                35
  STAGE IV                 8                36
[1] 11  2
[1] 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     3   3  30  19
  3Q LOSS WILD-TYPE  20  90 166 100
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               3                20
  T2               3                90
  T3              30               166
  T4              19               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q LOSS MUTATED    14  15  16   9
  3Q LOSS WILD-TYPE 116 104  70  79
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              14               116
  N1              15               104
  N2              16                70
  N3               9                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    48   7
  3Q LOSS WILD-TYPE 341  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     48    7
  3Q LOSS WILD-TYPE  341   23
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              48               341
  1               7                23
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    21  35
  3Q LOSS WILD-TYPE 137 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     21   35
  3Q LOSS WILD-TYPE  137  248
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              21               137
  MALE                35               248
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    43   8
  3Q LOSS WILD-TYPE 279  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     43    8
  3Q LOSS WILD-TYPE  279   68
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               43               279
  YES               8                68
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  3Q LOSS MUTATED                                          3
  3Q LOSS WILD-TYPE                                       10
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  3Q LOSS MUTATED                                       3
  3Q LOSS WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                       23
  3Q LOSS WILD-TYPE                                                    140
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  3Q LOSS MUTATED                                                   2
  3Q LOSS WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                                  13
  3Q LOSS WILD-TYPE                                                                69
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  3Q LOSS MUTATED                                                    0
  3Q LOSS WILD-TYPE                                                  8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  3Q LOSS MUTATED                                                 12
  3Q LOSS WILD-TYPE                                               67
D47V9, multiclass
                                                                   clus
vv                                                                  3Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         23
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              13
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               12
                                                                   clus
vv                                                                  3Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          140
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                69
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 67
[1] 7 2
[1] TRUE
[1] "dimension of 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    44   3   2   2
  3Q LOSS WILD-TYPE 305  15  17  23
D47V10, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              44               305
  R1               3                15
  R2               2                17
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED       9                         1
  3Q LOSS WILD-TYPE    79                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           0    41
  3Q LOSS WILD-TYPE                                         1   237
D47V12, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                                   9                79
  BLACK OR AFRICAN AMERICAN                               1                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  41               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  40
  3Q LOSS WILD-TYPE   4 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   40
  3Q LOSS WILD-TYPE    4  276
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              40               276
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    91  65
  4P LOSS WILD-TYPE 155 104
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              156               259 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               65               104 
$`4P LOSS MUTATED`
TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 
       47.05        79.07         0.23         9.86        26.93        58.03 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4279 
       11.01         9.44         6.61         4.08         9.67         9.57 
TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7717 
       17.29         9.17        31.20         9.21        35.24        18.15 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 
       28.73         9.07        33.21        37.25         0.69         9.60 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        19.96         2.20        15.58         7.40        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 
       22.19        17.52        14.04        14.79         3.72         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 
        9.21        20.22        26.73        24.79         9.86        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
        7.53        34.98         1.48         0.72         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
       20.65        21.44        13.02        13.35        11.21        12.59 
TCGA-CD-8526 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A487 
       12.53        11.64        15.39        12.07        12.82        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
       11.31        12.43        11.61        12.20        20.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 
        8.05        54.08         4.01        19.07        12.03        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5725 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 
        7.07        30.97        15.02        19.13        20.55        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YU 
       10.26        15.22        11.31        19.50        18.21        16.44 
TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 
       11.31        19.96         0.62         7.99        11.38        14.07 
TCGA-FP-8099 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       17.06         5.52        63.06        26.47         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP 
       18.15        28.96        22.82        22.75        25.81         8.98 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
        6.58         0.26         2.10        12.95        23.84        21.17 
TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IP-7968 
       33.40        18.81        12.46         6.44         6.74         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        5.56        63.62        14.04        45.67        18.21         6.08 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
        9.24        11.05        16.67        37.91       115.69         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       35.61         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       21.73         7.73        46.26        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X 
       17.85        73.41        39.45        18.74        42.64         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
        9.73        55.56         9.04         4.54        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       11.24        38.93        32.94        54.12        16.14        27.55 

$`4P LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU TCGA-B7-5816 
       21.99        22.98        16.24        20.15        27.35        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.70        19.56         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4280 
       18.35        30.90         4.08         9.34         6.18         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        8.98        40.21        30.90        44.94        21.90        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7958 
       35.84        33.63        39.78        15.32         3.45        29.56 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44        29.59        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 
       29.42         6.18        13.08         0.26         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        6.28         7.53        31.96        32.58        20.88         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       34.13        13.87         6.08        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
        8.98        14.17         0.53        28.34        32.52         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
       20.42         1.15        16.14         5.13        13.41        13.15 
TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       13.18        12.10        12.76         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CD-A4MI 
       12.39        12.59        12.43         6.31         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 
       12.62         3.02        27.02        15.95         1.02        14.01 
TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
       29.98         0.00         9.01        12.00         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       25.71        12.66        20.91        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
       17.85        13.35        15.98        12.79        12.36        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        17.19        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        4.34         7.13        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       19.53        22.29        59.54         5.03        13.58         0.56 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8244 TCGA-HU-8602 
        6.21        77.29        52.21        30.51        24.39        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20         3.25        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.51        20.25        29.00        23.80        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       36.36         3.45         3.39        18.38        13.35        19.53 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64        36.95         3.72        19.73         8.52        74.53 
TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        4.60         8.61         5.13       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       48.79        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E 
       13.35        29.59        64.57        14.33        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A923 
       61.22        20.81        32.88         1.71        60.85         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 
       55.43         6.58         5.72        66.81         2.66        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       43.66        28.41        17.13        26.04        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.23              0.00 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           115.69            122.30 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           13.775            15.680 
[1] "0.2 - 115.7 (13.8)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         0        3       12       16        19        17
  4P LOSS WILD-TYPE       2       13       29       16        21        39
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           1         34         25         18       13
  4P LOSS WILD-TYPE         2         47         38         21       31
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                13
  STAGE IB                12                29
  STAGE II                16                16
  STAGE IIA               19                21
  STAGE IIB               17                39
  STAGE III                1                 2
  STAGE IIIA              34                47
  STAGE IIIB              25                38
  STAGE IIIC              18                21
  STAGE IV                13                31
[1] 11  2
[1] 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     5  29  87  42
  4P LOSS WILD-TYPE  18  64 109  77
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               5                18
  T2              29                64
  T3              87               109
  T4              42                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4P LOSS MUTATED   44 41 38 35
  4P LOSS WILD-TYPE 86 78 48 53
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              44                86
  N1              41                78
  N2              38                48
  N3              35                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   150   7
  4P LOSS WILD-TYPE 239  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    150    7
  4P LOSS WILD-TYPE  239   23
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             150               239
  1               7                23
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    58 109
  4P LOSS WILD-TYPE 100 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     58  109
  4P LOSS WILD-TYPE  100  174
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              58               100
  MALE               109               174
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   119  32
  4P LOSS WILD-TYPE 203  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    119   32
  4P LOSS WILD-TYPE  203   44
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO              119               203
  YES              32                44
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  4P LOSS MUTATED                                          7
  4P LOSS WILD-TYPE                                        6
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  4P LOSS MUTATED                                      21
  4P LOSS WILD-TYPE                                    51
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                       57
  4P LOSS WILD-TYPE                                                    106
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  4P LOSS MUTATED                                                   7
  4P LOSS WILD-TYPE                                                14
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                                  38
  4P LOSS WILD-TYPE                                                                44
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  4P LOSS MUTATED                                                    2
  4P LOSS WILD-TYPE                                                  6
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  4P LOSS MUTATED                                                 35
  4P LOSS WILD-TYPE                                               44
D48V9, multiclass
                                                                   clus
vv                                                                  4P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          21
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         57
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               35
                                                                   clus
vv                                                                  4P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            51
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          106
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                44
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 44
[1] 7 2
[1] TRUE
[1] "dimension of 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   128   7   6   9
  4P LOSS WILD-TYPE 221  11  13  16
D48V10, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0             128               221
  R1               7                11
  R2               6                13
  RX               9                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"
D48V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED      37                         5
  4P LOSS WILD-TYPE    51                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           0   101
  4P LOSS WILD-TYPE                                         1   177
D48V12, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                                  37                51
  BLACK OR AFRICAN AMERICAN                               5                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 101               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"
D48V13, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     2 116
  4P LOSS WILD-TYPE   3 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2  116
  4P LOSS WILD-TYPE    3  200
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             116               200
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    88  68
  4Q LOSS WILD-TYPE 158 101
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              156               259 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               68               101 
$`4Q LOSS MUTATED`
TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 
       47.05        79.07         0.23         9.86        26.93        58.03 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6456 
       11.01         9.44         6.61         4.08         9.67        17.29 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 
       19.33         9.17        31.20        35.24        18.15        28.73 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
        9.07        33.21        37.25        14.43         0.69         9.60 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        19.96         2.20        15.58         7.40        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 
       22.19        17.52        14.04        14.79         3.72         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 
        9.21        20.22        26.73        24.79         9.86        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
        7.53        34.98         1.48         0.72         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 
       20.65         1.15        21.44        13.02        13.35        11.21 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.59        12.53         7.17        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
       12.82        12.30        11.31        12.43        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 
       20.02         7.99         8.05        54.08         4.01        19.07 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
       12.03        18.97        30.97        15.02         4.01        69.04 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       19.13        20.55        17.19        10.26        15.22        15.98 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A 
       11.31        19.50        18.21        16.44        11.31        19.96 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF 
        0.62         7.99        11.38        14.07        17.06         5.52 
TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-A4GD 
       63.06         1.51         5.92        18.15        22.82        22.75 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        8.98         6.58         0.26         2.10        12.95        23.84 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RP 
       21.17        33.40        18.81         3.39        12.46         6.44 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        6.74        10.62         2.53        14.04        45.67        18.21 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
        6.08         9.24        11.05        16.67        37.91       115.69 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94        35.61         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       43.36        21.73         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N 
        2.70        17.85        13.35        73.41        39.45        18.74 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O 
        9.50         9.73        55.56         9.04         4.54        21.04 
TCGA-VQ-A94R TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       42.54        32.94        54.12        16.14        27.55        12.43 

$`4Q LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU TCGA-B7-5816 
       21.99        22.98        16.24        20.15        27.35        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.70        19.56         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       18.35        30.90         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 
       36.16        35.84        33.63        39.78        15.32         3.45 
TCGA-BR-7958 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       29.56        11.44        29.59        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 
       29.42         6.18        13.08         0.26         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        6.28         7.53        31.96        32.58        20.88         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       34.13        13.87         6.08        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
        8.98        14.17         0.53        28.34        32.52         0.46 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
       20.42        16.14         5.13        13.41        13.15        13.18 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.10        12.76        12.33        12.30        12.39        12.59 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       12.43         6.31         6.58        11.77        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 
       27.02        15.95         1.02        14.01        29.98         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01         7.07        12.00         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       65.10        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 
       18.84        18.54        18.61        17.85        13.35        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 
       12.36        12.33        24.72        16.80        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 
       15.65         8.38         4.34         7.13        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         3.48        19.53        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
       13.58         0.56         6.21        77.29        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
       26.47        24.39        28.96        22.32        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       20.25        29.00        23.80        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR 
        3.45        18.38        13.35        19.53        12.59         6.51 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       11.70        15.75        13.51         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       36.95         3.72        19.73         8.52        74.53         4.60 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       37.41        38.14        37.22        30.97        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       64.57        14.33        11.70        21.83        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 
       32.88         1.71        42.64        60.85         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58         5.72        66.81         2.66        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 
       43.66        28.41        38.93        17.13        26.04        17.26 
TCGA-ZQ-A9CR 
        0.79 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.23              0.00 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           115.69            122.30 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            13.35             15.95 
[1] "0.2 - 115.7 (13.3)" "0.0 - 122.3 (15.9)"
[1] "hr=" "1.3"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         0        3       10       15        17        21
  4Q LOSS WILD-TYPE       2       13       31       17        23        35
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           2         32         25         18       14
  4Q LOSS WILD-TYPE         1         49         38         21       30
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                13
  STAGE IB                10                31
  STAGE II                15                17
  STAGE IIA               17                23
  STAGE IIB               21                35
  STAGE III                2                 1
  STAGE IIIA              32                49
  STAGE IIIB              25                38
  STAGE IIIC              18                21
  STAGE IV                14                30
[1] 11  2
[1] 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     4  32  81  44
  4Q LOSS WILD-TYPE  19  61 115  75
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               4                19
  T2              32                61
  T3              81               115
  T4              44                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4Q LOSS MUTATED   40 45 37 35
  4Q LOSS WILD-TYPE 90 74 49 53
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              40                90
  N1              45                74
  N2              37                49
  N3              35                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   149   8
  4Q LOSS WILD-TYPE 240  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    149    8
  4Q LOSS WILD-TYPE  240   22
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             149               240
  1               8                22
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    61 104
  4Q LOSS WILD-TYPE  97 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     61  104
  4Q LOSS WILD-TYPE   97  179
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              61                97
  MALE               104               179
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   121  30
  4Q LOSS WILD-TYPE 201  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    121   30
  4Q LOSS WILD-TYPE  201   46
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              121               201
  YES              30                46
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  4Q LOSS MUTATED                                          7
  4Q LOSS WILD-TYPE                                        6
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  4Q LOSS MUTATED                                      20
  4Q LOSS WILD-TYPE                                    52
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                       57
  4Q LOSS WILD-TYPE                                                    106
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  4Q LOSS MUTATED                                                   7
  4Q LOSS WILD-TYPE                                                14
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                                  39
  4Q LOSS WILD-TYPE                                                                43
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  4Q LOSS MUTATED                                                    2
  4Q LOSS WILD-TYPE                                                  6
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  4Q LOSS MUTATED                                                 33
  4Q LOSS WILD-TYPE                                               46
D49V9, multiclass
                                                                   clus
vv                                                                  4Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          20
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         57
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               33
                                                                   clus
vv                                                                  4Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            52
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          106
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                43
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 46
[1] 7 2
[1] TRUE
[1] "dimension of 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   127   7   7   7
  4Q LOSS WILD-TYPE 222  11  12  18
D49V10, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             127               222
  R1               7                11
  R2               7                12
  RX               7                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"
D49V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED      36                         5
  4Q LOSS WILD-TYPE    52                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           0   103
  4Q LOSS WILD-TYPE                                         1   175
D49V12, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                                  36                52
  BLACK OR AFRICAN AMERICAN                               5                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 103               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"
D49V13, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     2 116
  4Q LOSS WILD-TYPE   3 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2  116
  4Q LOSS WILD-TYPE    3  200
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             116               200
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    30  32
  5P LOSS WILD-TYPE 216 137
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               62               353 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               32               137 
$`5P LOSS MUTATED`
TCGA-MX-A663 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6458 
        9.86        11.01         9.44         6.61         9.67        19.33 
TCGA-BR-6565 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8483 
        9.17        29.56        33.21         2.20        14.04         5.39 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        9.86        10.68         7.53        34.98         1.48         0.72 
TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-8535 TCGA-CD-A4MH TCGA-CG-4440 TCGA-CG-4449 
       21.44        13.15        12.82        12.20         4.01        19.07 
TCGA-D7-6520 TCGA-D7-6815 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF 
       18.84        15.98         7.99        72.23         0.56         5.52 
TCGA-FP-A9TM TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GP 
        6.21         5.92         0.76         3.25        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RL 
        6.58        23.84        21.17        36.36        18.81        13.35 
TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A8MW 
        6.44        63.62        37.64         8.52         6.08        37.91 
TCGA-SW-A7EB TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
        5.79        13.02         7.73        22.19        12.79         2.70 
TCGA-VQ-A8PS TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O 
       13.35         1.71         9.73        55.56         9.04        21.04 
TCGA-VQ-A94R TCGA-ZQ-A9CR 
       42.54         0.79 

$`5P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       20.15        27.35        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       31.96        32.58        20.88         8.22        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.02        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
        7.99         8.05        54.08        14.01        29.98        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
       19.96         7.13         0.62        14.47        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.03        13.58        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.82        21.07        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20        22.75        25.81        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 
       23.80        14.07        15.68        33.40         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       18.38        12.46        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       74.53         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       57.44         8.94        35.61        16.87        19.04         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.25        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       37.41        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.50        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       42.64        60.85         9.50         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58         5.72        66.81         2.66        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.56              0.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            72.23            122.30 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            10.27             15.95 
[1] "0.6 - 72.2 (10.3)"  "0.0 - 122.3 (15.9)"
[1] "hr=" "1.7"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         0        3        1        2         5        12
  5P LOSS WILD-TYPE       2       13       40       30        35        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           1         16          8          6        5
  5P LOSS WILD-TYPE         2         65         55         33       39
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                13
  STAGE IB                 1                40
  STAGE II                 2                30
  STAGE IIA                5                35
  STAGE IIB               12                44
  STAGE III                1                 2
  STAGE IIIA              16                65
  STAGE IIIB               8                55
  STAGE IIIC               6                33
  STAGE IV                 5                39
[1] 11  2
[1] 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     5   8  27  21
  5P LOSS WILD-TYPE  18  85 169  98
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               5                18
  T2               8                85
  T3              27               169
  T4              21                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P LOSS MUTATED    11  23  13  12
  5P LOSS WILD-TYPE 119  96  73  76
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              11               119
  N1              23                96
  N2              13                73
  N3              12                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    56   4
  5P LOSS WILD-TYPE 333  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     56    4
  5P LOSS WILD-TYPE  333   26
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              56               333
  1               4                26
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    21  42
  5P LOSS WILD-TYPE 137 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     21   42
  5P LOSS WILD-TYPE  137  241
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              21               137
  MALE                42               241
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    50   9
  5P LOSS WILD-TYPE 272  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     50    9
  5P LOSS WILD-TYPE  272   67
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               50               272
  YES               9                67
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  5P LOSS MUTATED                                          2
  5P LOSS WILD-TYPE                                       11
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  5P LOSS MUTATED                                       4
  5P LOSS WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                       22
  5P LOSS WILD-TYPE                                                    141
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  5P LOSS MUTATED                                                   3
  5P LOSS WILD-TYPE                                                18
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                                  12
  5P LOSS WILD-TYPE                                                                70
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  5P LOSS MUTATED                                                    1
  5P LOSS WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  5P LOSS MUTATED                                                 19
  5P LOSS WILD-TYPE                                               60
D50V9, multiclass
                                                                   clus
vv                                                                  5P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               19
                                                                   clus
vv                                                                  5P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of 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    48   2   4   3
  5P LOSS WILD-TYPE 301  16  15  22
D50V10, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              48               301
  R1               2                16
  R2               4                15
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5P LOSS MUTATED      16                         5
  5P LOSS WILD-TYPE    72                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           0    37
  5P LOSS WILD-TYPE                                         1   241
D50V12, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                                  16                72
  BLACK OR AFRICAN AMERICAN                               5                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  37               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  47
  5P LOSS WILD-TYPE   5 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   47
  5P LOSS WILD-TYPE    5  269
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              47               269
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    56  50
  5Q LOSS WILD-TYPE 190 119
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              106               309 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               50               119 
$`5Q LOSS MUTATED`
TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       47.05         9.86        27.35        11.01         9.44         6.61 
TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7716 
        9.67        19.33         9.17         9.21        35.24        39.78 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
        3.45        29.56        33.21        29.42         2.66         2.20 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 
       14.04        14.79         5.39        24.79         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4QI 
       10.68         7.53        34.98         1.48         0.72        21.44 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8533 
       13.15        13.18        12.59        12.53        12.33        15.39 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4440 
       12.82        11.31        11.61        12.20        27.02         4.01 
TCGA-CG-4449 TCGA-CG-5718 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6527 TCGA-D7-6815 
       19.07        36.00        20.91        18.84        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-EQ-8122 
       12.79        12.33        24.72        11.31        22.29         7.99 
TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HU-8243 TCGA-HU-8610 
       72.23         0.56         5.52         6.21         5.92         0.76 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H4 
        3.25        22.75        11.77         8.98         6.58        23.84 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RP 
       21.17        33.40        36.36        18.81        13.35         6.44 
TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       15.75        63.62        37.64        18.21         8.52         6.08 
TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV 
        8.61        37.91         8.94         5.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       13.02        43.36         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Y 
        2.70        17.85        13.35         1.71        42.64         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
       55.56         9.04         2.01         4.54        21.04        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-ZQ-A9CR 
       43.66        38.93        17.13         0.79 

$`5Q LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       26.93        58.03        26.70        11.70        19.56         9.47 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       35.84        33.63        18.15        15.32        28.73         9.07 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
       32.25         8.05         0.56        19.96        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-A44T 
        7.53        26.73        31.96        32.58        20.88        34.13 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       13.87         6.08        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65        20.42         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.41        13.02        13.35        11.21        12.10        12.76 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 
        7.17        12.30        12.39        12.59        11.64        12.07 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI 
       12.43         6.31        12.30        12.43         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 
        8.05        54.08        14.01        29.98        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
        7.99        25.71        12.66        19.13        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 
       18.61        17.85        13.35        17.19        15.22        12.36 
TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       11.31        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 
       22.29        17.06        59.54         5.03        13.58        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
       18.15        28.96        22.32        22.82        21.07        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GJ 
        5.59        24.26        22.68        24.20        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
       12.95        29.00        23.80        14.07        15.68         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39        18.38        12.46        19.53         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        11.70        13.51         2.53         5.56 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZI 
       36.95         3.72        19.73        14.04        45.67        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60         9.24        11.05         5.13        16.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8E3 
       16.87        19.04         0.92        48.79        18.48        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       37.41        38.14        37.22        30.97        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        18.74        20.81        32.88        60.85         9.50 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T 
       55.43         6.58         5.72        66.81         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        28.41        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.56              0.00 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            72.23            122.30 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            12.79             16.14 
[1] "0.6 - 72.2 (12.8)"  "0.0 - 122.3 (16.1)"
[1] "hr=" "1.4"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         0        4        6        8         6        16
  5Q LOSS WILD-TYPE       2       12       35       24        34        40
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           1         35         11         10        7
  5Q LOSS WILD-TYPE         2         46         52         29       37
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 4                12
  STAGE IB                 6                35
  STAGE II                 8                24
  STAGE IIA                6                34
  STAGE IIB               16                40
  STAGE III                1                 2
  STAGE IIIA              35                46
  STAGE IIIB              11                52
  STAGE IIIC              10                29
  STAGE IV                 7                37
[1] 11  2
[1] 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     6  18  52  30
  5Q LOSS WILD-TYPE  17  75 144  89
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               6                17
  T2              18                75
  T3              52               144
  T4              30                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q LOSS MUTATED    23  37  24  20
  5Q LOSS WILD-TYPE 107  82  62  68
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              23               107
  N1              37                82
  N2              24                62
  N3              20                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   100   5
  5Q LOSS WILD-TYPE 289  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    100    5
  5Q LOSS WILD-TYPE  289   25
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0             100               289
  1               5                25
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    38  70
  5Q LOSS WILD-TYPE 120 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     38   70
  5Q LOSS WILD-TYPE  120  213
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              38               120
  MALE                70               213
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    83  20
  5Q LOSS WILD-TYPE 239  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     83   20
  5Q LOSS WILD-TYPE  239   56
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               83               239
  YES              20                56
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  5Q LOSS MUTATED                                          3
  5Q LOSS WILD-TYPE                                       10
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  5Q LOSS MUTATED                                       6
  5Q LOSS WILD-TYPE                                    66
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                       35
  5Q LOSS WILD-TYPE                                                    128
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  5Q LOSS MUTATED                                                   5
  5Q LOSS WILD-TYPE                                                16
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                                  23
  5Q LOSS WILD-TYPE                                                                59
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  5Q LOSS MUTATED                                                    2
  5Q LOSS WILD-TYPE                                                  6
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  5Q LOSS MUTATED                                                 34
  5Q LOSS WILD-TYPE                                               45
D51V9, multiclass
                                                                   clus
vv                                                                  5Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         35
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              23
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               34
                                                                   clus
vv                                                                  5Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          128
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                59
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 45
[1] 7 2
[1] TRUE
[1] "dimension of 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    86   4   6   3
  5Q LOSS WILD-TYPE 263  14  13  22
D51V10, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              86               263
  R1               4                14
  R2               6                13
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED      26                         5
  5Q LOSS WILD-TYPE    62                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           1    66
  5Q LOSS WILD-TYPE                                         0   212
D51V12, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                                  26                62
  BLACK OR AFRICAN AMERICAN                               5                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  66               212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0  77
  5Q LOSS WILD-TYPE   5 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   77
  5Q LOSS WILD-TYPE    5  239
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              77               239
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    28  20
  6P LOSS WILD-TYPE 218 149
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               48               367 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               20               149 
$`6P LOSS MUTATED`
TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-7716 
       16.24         9.86        27.35         6.18        17.29        39.78 
TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-8530 
       34.98         0.72        13.51        20.65         1.15        12.39 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A48A TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 
       11.64        12.82        12.43         1.02        12.03        15.02 
TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-A6EX 
       12.66        18.84        18.54        13.35        15.98        11.31 
TCGA-D7-A6F2 TCGA-F1-A72C TCGA-FP-8099 TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GH 
       15.65        11.38        17.06        26.47        22.75        11.77 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT 
        6.58        12.95        33.40        13.35         6.44        10.62 
TCGA-IN-A7NU TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N5 TCGA-VQ-A8DU TCGA-VQ-A8PY 
       11.70         6.08        16.67        57.44         5.46        14.33 
TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       20.81         9.04         4.54        54.12        16.14        27.55 

$`6P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       26.93        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.84        33.63        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       29.42         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        32.52         0.46        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.33        12.30        12.59        15.39        12.07        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        12.30        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
        7.07        12.00        30.97         6.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 
       69.04        21.07         7.99        25.71        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       20.55        18.61        17.85        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       26.43        11.24        11.44        20.32        22.29         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51        20.25         0.26         2.10        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       18.81         3.39        18.38        12.46        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         6.51        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       63.62        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       23.41        15.65        13.35        29.59        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
        2.01        55.43         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       38.93        32.94        17.13        26.04        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.72              0.00 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            57.44            122.30 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            13.35             15.39 
[1] "0.7 - 57.4 (13.3)"  "0.0 - 122.3 (15.4)"
[1] "hr=" "1.2"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         0        1        5        2         4         8
  6P LOSS WILD-TYPE       2       15       36       30        36        48
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           1         13          8          1        4
  6P LOSS WILD-TYPE         2         68         55         38       40
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                15
  STAGE IB                 5                36
  STAGE II                 2                30
  STAGE IIA                4                36
  STAGE IIB                8                48
  STAGE III                1                 2
  STAGE IIIA              13                68
  STAGE IIIB               8                55
  STAGE IIIC               1                38
  STAGE IV                 4                40
[1] 11  2
[1] 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     2  11  28   9
  6P LOSS WILD-TYPE  21  82 168 110
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               2                21
  T2              11                82
  T3              28               168
  T4               9               110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P LOSS MUTATED    14  14  12   7
  6P LOSS WILD-TYPE 116 105  74  81
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              14               116
  N1              14               105
  N2              12                74
  N3               7                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"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    44   2
  6P LOSS WILD-TYPE 345  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     44    2
  6P LOSS WILD-TYPE  345   28
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              44               345
  1               2                28
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    14  36
  6P LOSS WILD-TYPE 144 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     14   36
  6P LOSS WILD-TYPE  144  247
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              14               144
  MALE                36               247
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    37   9
  6P LOSS WILD-TYPE 285  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     37    9
  6P LOSS WILD-TYPE  285   67
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               37               285
  YES               9                67
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  6P LOSS MUTATED                                          1
  6P LOSS WILD-TYPE                                       12
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  6P LOSS MUTATED                                       6
  6P LOSS WILD-TYPE                                    66
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                       19
  6P LOSS WILD-TYPE                                                    144
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  6P LOSS MUTATED                                                   1
  6P LOSS WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                                   5
  6P LOSS WILD-TYPE                                                                77
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  6P LOSS MUTATED                                                    0
  6P LOSS WILD-TYPE                                                  8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  6P LOSS MUTATED                                                 17
  6P LOSS WILD-TYPE                                               62
D52V9, multiclass
                                                                   clus
vv                                                                  6P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               17
                                                                   clus
vv                                                                  6P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                77
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 62
[1] 7 2
[1] TRUE
[1] "dimension of 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    43   0   2   3
  6P LOSS WILD-TYPE 306  18  17  22
D52V10, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              43               306
  R1               0                18
  R2               2                17
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6P LOSS MUTATED      11                         2
  6P LOSS WILD-TYPE    77                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           0    32
  6P LOSS WILD-TYPE                                         1   246
D52V12, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  32               246
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0  38
  6P LOSS WILD-TYPE   5 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   38
  6P LOSS WILD-TYPE    5  278
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              38               278
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    36  29
  6Q LOSS WILD-TYPE 210 140
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               65               350 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               29               140 
$`6Q LOSS MUTATED`
TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6565 
       16.24         9.86        27.35         6.18        17.29         9.17 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-8080 TCGA-BR-A4CQ TCGA-BR-A4J8 TCGA-BR-A4PD 
       39.78        15.32         9.60        34.98        13.51        20.65 
TCGA-BR-A4PF TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 
        1.15        11.21        12.10        12.39        11.64        12.82 
TCGA-CD-A48A TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 
       12.43        29.98        12.03         1.02        12.03        15.02 
TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-8570 
       12.66        18.84        18.54        13.35        15.98        24.72 
TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8099 
       14.66        11.31        15.65        19.96        11.38        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4H4 
       13.58         0.56        26.47        22.75         6.58        23.84 
TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A93J 
       33.40        13.35         6.44        10.62        11.70        36.95 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-VQ-A8DU 
       18.21         6.08        16.67       122.30        57.44         5.46 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 
       13.35        14.33        20.81         9.04         2.01         4.54 
TCGA-VQ-A94O TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       21.04        54.12        16.14        27.55         0.79 

$`6Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       26.93        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       33.63        18.15        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 
       13.02        13.15        13.18        13.35        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8533 
       12.53         7.17        12.33        12.30        12.59        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       12.07        12.43         6.31        12.30        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
        4.01        14.01        19.07         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
        7.07        12.00        30.97         6.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 
       69.04        21.07         7.99        25.71        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       20.55        18.61        17.85        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44        20.32        22.29         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF 
       19.53        14.07        22.29        59.54         5.03         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
       19.53         6.74        12.59         6.51        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        37.64         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       14.04        45.67         8.52        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         8.61         5.13        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        5.79         0.92        48.79        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        29.59        64.57        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       21.83        61.22        18.74        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 
       60.85         9.50         9.73        55.56        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        66.81         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        17.13        26.04 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.56              0.00 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           122.30            116.38 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           13.580            15.485 
[1] "0.6 - 122.3 (13.6)" "0.0 - 116.4 (15.5)"
[1] "hr=" "1.2"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         0        1        5        5         4        12
  6Q LOSS WILD-TYPE       2       15       36       27        36        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           1         17         10          5        4
  6Q LOSS WILD-TYPE         2         64         53         34       40
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                15
  STAGE IB                 5                36
  STAGE II                 5                27
  STAGE IIA                4                36
  STAGE IIB               12                44
  STAGE III                1                 2
  STAGE IIIA              17                64
  STAGE IIIB              10                53
  STAGE IIIC               5                34
  STAGE IV                 4                40
[1] 11  2
[1] 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     2  14  39  13
  6Q LOSS WILD-TYPE  21  79 157 106
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               2                21
  T2              14                79
  T3              39               157
  T4              13               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q LOSS MUTATED    16  21  17  12
  6Q LOSS WILD-TYPE 114  98  69  76
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              16               114
  N1              21                98
  N2              17                69
  N3              12                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    60   2
  6Q LOSS WILD-TYPE 329  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     60    2
  6Q LOSS WILD-TYPE  329   28
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              60               329
  1               2                28
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    20  49
  6Q LOSS WILD-TYPE 138 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     20   49
  6Q LOSS WILD-TYPE  138  234
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              20               138
  MALE                49               234
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    50  12
  6Q LOSS WILD-TYPE 272  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     50   12
  6Q LOSS WILD-TYPE  272   64
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               50               272
  YES              12                64
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  6Q LOSS MUTATED                                          1
  6Q LOSS WILD-TYPE                                       12
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  6Q LOSS MUTATED                                       8
  6Q LOSS WILD-TYPE                                    64
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                       24
  6Q LOSS WILD-TYPE                                                    139
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  6Q LOSS MUTATED                                                   3
  6Q LOSS WILD-TYPE                                                18
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                                  10
  6Q LOSS WILD-TYPE                                                                72
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  6Q LOSS MUTATED                                                    0
  6Q LOSS WILD-TYPE                                                  8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  6Q LOSS MUTATED                                                 22
  6Q LOSS WILD-TYPE                                               57
D53V9, multiclass
                                                                   clus
vv                                                                  6Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         24
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              10
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               22
                                                                   clus
vv                                                                  6Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                72
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of 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    58   1   2   4
  6Q LOSS WILD-TYPE 291  17  17  21
D53V10, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              58               291
  R1               1                17
  R2               2                17
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6Q LOSS MUTATED      11                         3
  6Q LOSS WILD-TYPE    77                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           0    47
  6Q LOSS WILD-TYPE                                         1   231
D53V12, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               3                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  47               231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0  50
  6Q LOSS WILD-TYPE   5 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   50
  6Q LOSS WILD-TYPE    5  266
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              50               266
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    11   6
  7P LOSS WILD-TYPE 235 163
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               17               398 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6               163 
$`7P LOSS MUTATED`
TCGA-BR-4255 TCGA-BR-7723 TCGA-BR-8678 TCGA-CG-4438 TCGA-CG-4443 TCGA-D7-6820 
        4.08        28.73        24.79        54.08        29.98        11.31 
TCGA-D7-A6EX TCGA-FP-8631 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-IN-A6RN TCGA-RD-A8MW 
       11.31         0.56        11.77         6.58        19.53        37.91 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PJ TCGA-VQ-A91S 
       35.61         5.46        18.48         2.70        32.88 

$`7P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 
       20.15         9.86        27.35        26.93        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 
        1.02         7.99         8.05         4.01        14.01        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       22.29        17.06        59.54         5.03        13.58         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        12.46        13.35         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
        2.53         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79        13.25        13.02        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31        22.19         2.50        12.79        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        20.81         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.56              0.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            54.08            122.30 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           18.480            14.775 
[1] "0.6 - 54.1 (18.5)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         0        2        1        1         1         2
  7P LOSS WILD-TYPE       2       14       40       31        39        54
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           0          5          3          0        2
  7P LOSS WILD-TYPE         3         76         60         39       42
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                14
  STAGE IB                 1                40
  STAGE II                 1                31
  STAGE IIA                1                39
  STAGE IIB                2                54
  STAGE III                0                 3
  STAGE IIIA               5                76
  STAGE IIIB               3                60
  STAGE IIIC               0                39
  STAGE IV                 2                42
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P LOSS MUTATED     3   3   8   3
  7P LOSS WILD-TYPE  20  90 188 116
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               3                20
  T2               3                90
  T3               8               188
  T4               3               116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P LOSS MUTATED     3   5   8   1
  7P LOSS WILD-TYPE 127 114  78  87
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               3               127
  N1               5               114
  N2               8                78
  N3               1                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    15   1
  7P LOSS WILD-TYPE 374  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     15    1
  7P LOSS WILD-TYPE  374   29
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              15               374
  1               1                29
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     4  13
  7P LOSS WILD-TYPE 154 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      4   13
  7P LOSS WILD-TYPE  154  270
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               4               154
  MALE                13               270
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    10   4
  7P LOSS WILD-TYPE 312  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     10    4
  7P LOSS WILD-TYPE  312   72
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               10               312
  YES               4                72
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  7P LOSS MUTATED                                          0
  7P LOSS WILD-TYPE                                       13
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  7P LOSS MUTATED                                       2
  7P LOSS WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                        4
  7P LOSS WILD-TYPE                                                    159
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  7P LOSS MUTATED                                                   0
  7P LOSS WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                                   5
  7P LOSS WILD-TYPE                                                                77
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  7P LOSS MUTATED                                                    0
  7P LOSS WILD-TYPE                                                  8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  7P LOSS MUTATED                                                  6
  7P LOSS WILD-TYPE                                               73
D54V9, multiclass
                                                                   clus
vv                                                                  7P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                6
                                                                   clus
vv                                                                  7P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         13
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          159
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                77
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 73
[1] 7 2
[1] TRUE
[1] "dimension of 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    15   0   1   1
  7P LOSS WILD-TYPE 334  18  18  24
D54V10, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              15               334
  R1               0                18
  R2               1                18
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED       3                         2
  7P LOSS WILD-TYPE    85                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           0     9
  7P LOSS WILD-TYPE                                         1   269
D54V12, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                                   3                85
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               269
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  11
  7P LOSS WILD-TYPE   5 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   11
  7P LOSS WILD-TYPE    5  305
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              11               305
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    18  10
  7Q LOSS WILD-TYPE 228 159
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               28               387 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10               159 
$`7Q LOSS MUTATED`
TCGA-BR-4255 TCGA-BR-7723 TCGA-BR-8369 TCGA-BR-8678 TCGA-BR-A4CS TCGA-CD-A486 
        4.08        28.73        14.04        24.79         1.48         6.31 
TCGA-CD-A48C TCGA-CG-4438 TCGA-CG-4443 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8575 
       11.61        54.08        29.98        15.98        11.31        18.21 
TCGA-D7-A6EX TCGA-FP-7829 TCGA-FP-8631 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU 
       11.31        19.53         0.56        22.75        11.77         6.58 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN TCGA-KB-A93H TCGA-RD-A8MW 
       21.17        33.40        18.38        19.53        37.64        37.91 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PJ 
       35.61         5.46        18.48         2.70 

$`7Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 
       20.15         9.86        27.35        26.93        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82        12.43        12.30        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02         7.99         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.22        12.79        12.36        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM 
       17.06        59.54         5.03        13.58         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       29.00        23.84        23.80        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
        3.45        18.81         3.39        12.46        13.35         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79        13.25        13.02        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31        22.19         2.50        12.79        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.56              0.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            54.08            122.30 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           18.295            14.660 
[1] "0.6 - 54.1 (18.3)"  "0.0 - 122.3 (14.7)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         1        2        1        1         3         7
  7Q LOSS WILD-TYPE       1       14       40       31        37        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           0          8          3          1        2
  7Q LOSS WILD-TYPE         3         73         60         38       42
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 2                14
  STAGE IB                 1                40
  STAGE II                 1                31
  STAGE IIA                3                37
  STAGE IIB                7                49
  STAGE III                0                 3
  STAGE IIIA               8                73
  STAGE IIIB               3                60
  STAGE IIIC               1                38
  STAGE IV                 2                42
[1] 11  2
[1] 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     4   4  18   3
  7Q LOSS WILD-TYPE  19  89 178 116
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               4                19
  T2               4                89
  T3              18               178
  T4               3               116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q LOSS MUTATED     6   8  12   3
  7Q LOSS WILD-TYPE 124 111  74  85
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               6               124
  N1               8               111
  N2              12                74
  N3               3                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"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    27   1
  7Q LOSS WILD-TYPE 362  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     27    1
  7Q LOSS WILD-TYPE  362   29
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              27               362
  1               1                29
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     9  20
  7Q LOSS WILD-TYPE 149 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      9   20
  7Q LOSS WILD-TYPE  149  263
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               9               149
  MALE                20               263
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    21   4
  7Q LOSS WILD-TYPE 301  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     21    4
  7Q LOSS WILD-TYPE  301   72
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               21               301
  YES               4                72
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  7Q LOSS MUTATED                                          0
  7Q LOSS WILD-TYPE                                       13
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  7Q LOSS MUTATED                                       2
  7Q LOSS WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                       10
  7Q LOSS WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  7Q LOSS MUTATED                                                   1
  7Q LOSS WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                                   5
  7Q LOSS WILD-TYPE                                                                77
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  7Q LOSS MUTATED                                                    0
  7Q LOSS WILD-TYPE                                                  8
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  7Q LOSS MUTATED                                                 11
  7Q LOSS WILD-TYPE                                               68
D55V9, multiclass
                                                                   clus
vv                                                                  7Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               11
                                                                   clus
vv                                                                  7Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         13
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                77
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 68
[1] 7 2
[1] TRUE
[1] "dimension of 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    25   0   1   1
  7Q LOSS WILD-TYPE 324  18  18  24
D55V10, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              25               324
  R1               0                18
  R2               1                18
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED       9                         1
  7Q LOSS WILD-TYPE    79                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           0    16
  7Q LOSS WILD-TYPE                                         1   262
D55V12, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                                   9                79
  BLACK OR AFRICAN AMERICAN                               1                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  16               262
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  23
  7Q LOSS WILD-TYPE   5 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   23
  7Q LOSS WILD-TYPE    5  293
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              23               293
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    51  35
  8P LOSS WILD-TYPE 195 134
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               86               329 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               35               134 
$`8P LOSS MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 
       47.05        22.98        58.03        19.56         9.44        18.35 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7958 
        9.17        25.61        12.16        39.78        28.73        29.56 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8680 TCGA-BR-8683 
        0.69        29.42        15.58        13.08        31.96         9.86 
TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF 
        8.22        13.87        12.89         0.72        13.51         1.15 
TCGA-BR-A4QI TCGA-CD-8526 TCGA-CD-8533 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 
       21.44        12.53        15.39        11.61        12.20         3.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-5724 
        7.99        54.08         4.01        29.98        19.07        12.03 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 
        4.01        69.04        12.66        18.54        10.26        15.22 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-D7-A74A 
       11.31        24.72        18.21        16.44        15.65        19.96 
TCGA-FP-8099 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GU TCGA-HU-A4HD 
       17.06         5.92        28.96         0.76         6.58        33.40 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        6.44         6.74        11.70        15.75         2.53         5.56 
TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV 
       36.95        14.04        45.67         9.24         8.61       122.30 
TCGA-RD-A8MW TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PC TCGA-VQ-A8PK 
       37.91        18.48        43.36        37.41        46.26        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A925 
        1.87        13.35        20.81         1.71        55.56         4.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       11.24        18.41        43.66        32.94        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K 
       27.55        12.43 

$`8P LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       27.35        26.93        26.70        11.70        11.01         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       39.12        26.10        32.78        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        33.63        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        33.21        37.25        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 
       29.59         9.60        32.25         8.05         0.56         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       26.73        24.79        32.58        20.88        10.68        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        20.42        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        11.31        12.43         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 
       20.02        27.02        15.95         1.02         8.05        14.01 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
        0.99       105.07        15.02        28.96        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        20.91        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85        13.35        17.19        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       12.36        12.33        16.80        19.50        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       22.29         8.38         4.34         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       14.07        22.29        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       12.46        13.35        19.53        12.59         6.51        10.62 
TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE 
       13.51        63.62        37.64         3.72        19.73        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW 
        8.52        74.53         6.08         4.60        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       16.67        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       48.79         5.46        13.25        13.02        21.73        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       37.22         7.73        30.97        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        12.79         2.70         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        61.22        18.74        32.88        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.50         9.73         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 
        5.72        66.81        21.04         2.66        42.54        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       38.93        17.13        26.04        17.26         0.79 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.69              0.00 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           122.30            116.38 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           15.615            14.470 
[1] "0.7 - 122.3 (15.6)" "0.0 - 116.4 (14.5)"
[1] "hr=" "1"  
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         1        4        4        5         4         9
  8P LOSS WILD-TYPE       1       12       37       27        36        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           0         17         23          9       12
  8P LOSS WILD-TYPE         3         64         40         30       32
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 4                12
  STAGE IB                 4                37
  STAGE II                 5                27
  STAGE IIA                4                36
  STAGE IIB                9                47
  STAGE III                0                 3
  STAGE IIIA              17                64
  STAGE IIIB              23                40
  STAGE IIIC               9                30
  STAGE IV                12                32
[1] 11  2
[1] 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     6  14  49  21
  8P LOSS WILD-TYPE  17  79 147  98
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               6                17
  T2              14                79
  T3              49               147
  T4              21                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P LOSS MUTATED    16  24  25  23
  8P LOSS WILD-TYPE 114  95  61  65
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              16               114
  N1              24                95
  N2              25                61
  N3              23                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    79   7
  8P LOSS WILD-TYPE 310  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     79    7
  8P LOSS WILD-TYPE  310   23
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              79               310
  1               7                23
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    19  72
  8P LOSS WILD-TYPE 139 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     19   72
  8P LOSS WILD-TYPE  139  211
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              19               139
  MALE                72               211
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    63  18
  8P LOSS WILD-TYPE 259  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     63   18
  8P LOSS WILD-TYPE  259   58
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               63               259
  YES              18                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  8P LOSS MUTATED                                          3
  8P LOSS WILD-TYPE                                       10
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  8P LOSS MUTATED                                       7
  8P LOSS WILD-TYPE                                    65
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                       33
  8P LOSS WILD-TYPE                                                    130
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  8P LOSS MUTATED                                                   1
  8P LOSS WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                                  23
  8P LOSS WILD-TYPE                                                                59
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  8P LOSS MUTATED                                                    1
  8P LOSS WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  8P LOSS MUTATED                                                 22
  8P LOSS WILD-TYPE                                               57
D56V9, multiclass
                                                                   clus
vv                                                                  8P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         33
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              23
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               22
                                                                   clus
vv                                                                  8P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                59
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of 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    71   4   6   2
  8P LOSS WILD-TYPE 278  14  13  23
D56V10, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              71               278
  R1               4                14
  R2               6                13
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8P LOSS MUTATED      16                         3
  8P LOSS WILD-TYPE    72                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           1    56
  8P LOSS WILD-TYPE                                         0   222
D56V12, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                                  16                72
  BLACK OR AFRICAN AMERICAN                               3                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  56               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     2  56
  8P LOSS WILD-TYPE   3 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2   56
  8P LOSS WILD-TYPE    3  260
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              56               260
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    20  16
  8Q LOSS WILD-TYPE 226 153
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               36               379 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               16               153 
$`8Q LOSS MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-BR-4191 TCGA-BR-6705 TCGA-BR-8286 TCGA-BR-A4J8 
       47.05        22.98        18.35        25.61        29.42        13.51 
TCGA-BR-A4QI TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4443 
       21.44        11.61        12.20         7.99         4.01        29.98 
TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8570 TCGA-FP-8099 
       12.03        18.54        10.26        15.22        24.72        17.06 
TCGA-HU-8249 TCGA-HU-A4GU TCGA-IN-A7NU TCGA-IN-AB1V TCGA-R5-A805 TCGA-RD-A7BT 
       28.96         6.58        11.70        15.75         9.24         8.61 
TCGA-RD-A8MV TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PY 
      122.30        18.48        37.41        17.85         1.87        14.33 
TCGA-VQ-A91U TCGA-VQ-A925 TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6J 
        1.71         4.54        11.24        32.94        54.12        27.55 

$`8Q LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       27.35        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
       12.43         6.31        12.30        11.31        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 
        1.02         8.05        54.08        14.01        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       30.51        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       74.53         6.08         4.60        11.05         5.13        16.67 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.25        13.02        43.36        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       16.31        22.19         2.50        12.79         2.70         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       23.41        15.65        13.35        29.59        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       39.45        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       32.88        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        9.04         2.01        55.43         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       21.04         2.66        42.54        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       38.93        17.13        26.04        16.14        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.71              0.00 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           122.30            116.38 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           16.405            14.660 
[1] "1.7 - 122.3 (16.4)" "0.0 - 116.4 (14.7)"
[1] "hr=" "1"  
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         0        2        2        2         3         4
  8Q LOSS WILD-TYPE       2       14       39       30        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           0          5         11          0        5
  8Q LOSS WILD-TYPE         3         76         52         39       39
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                14
  STAGE IB                 2                39
  STAGE II                 2                30
  STAGE IIA                3                37
  STAGE IIB                4                52
  STAGE III                0                 3
  STAGE IIIA               5                76
  STAGE IIIB              11                52
  STAGE IIIC               0                39
  STAGE IV                 5                39
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED     2   6  26   2
  8Q LOSS WILD-TYPE  21  87 170 117
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               2                21
  T2               6                87
  T3              26               170
  T4               2               117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q LOSS MUTATED     8   8  11   9
  8Q LOSS WILD-TYPE 122 111  75  79
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               8               122
  N1               8               111
  N2              11                75
  N3               9                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    33   3
  8Q LOSS WILD-TYPE 356  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     33    3
  8Q LOSS WILD-TYPE  356   27
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              33               356
  1               3                27
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     8  29
  8Q LOSS WILD-TYPE 150 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      8   29
  8Q LOSS WILD-TYPE  150  254
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               8               150
  MALE                29               254
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    25   8
  8Q LOSS WILD-TYPE 297  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     25    8
  8Q LOSS WILD-TYPE  297   68
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               25               297
  YES               8                68
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  8Q LOSS MUTATED                                          1
  8Q LOSS WILD-TYPE                                       12
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  8Q LOSS MUTATED                                       5
  8Q LOSS WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                       10
  8Q LOSS WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  8Q LOSS MUTATED                                                   0
  8Q LOSS WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                                  12
  8Q LOSS WILD-TYPE                                                                70
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  8Q LOSS MUTATED                                                    1
  8Q LOSS WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  8Q LOSS MUTATED                                                  7
  8Q LOSS WILD-TYPE                                               72
D57V9, multiclass
                                                                   clus
vv                                                                  8Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                7
                                                                   clus
vv                                                                  8Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 72
[1] 7 2
[1] TRUE
[1] "dimension of 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    28   0   4   2
  8Q LOSS WILD-TYPE 321  18  15  23
D57V10, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              28               321
  R1               0                18
  R2               4                15
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8Q LOSS MUTATED       5                         2
  8Q LOSS WILD-TYPE    83                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           1    22
  8Q LOSS WILD-TYPE                                         0   256
D57V12, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                                   5                83
  BLACK OR AFRICAN AMERICAN                               2                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  22               256
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  20
  8Q LOSS WILD-TYPE   5 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   20
  8Q LOSS WILD-TYPE    5  296
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              20               296
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    80  62
  9P LOSS WILD-TYPE 166 107
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              142               273 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               62               107 
$`9P LOSS MUTATED`
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4191 
       27.35        26.93        58.03        11.01         9.44        18.35 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7197 
        4.08         9.67        13.68        19.33        31.20         9.21 
TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 
       35.24        39.78        18.15        28.73         3.45        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 
       11.44         0.69        19.96        22.19        17.52        14.04 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-8686 
        5.39        25.18         9.21        20.22         9.86        20.88 
TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 
        8.22        13.87        34.98         1.48         0.72         0.66 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 
       13.51        20.65         1.15        13.02        13.15        11.21 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 
       12.76        12.59        12.53         7.17        11.64        15.39 
TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 
       12.07         6.31        11.61         3.02        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5718 
       29.98        19.07        12.03        18.97        12.00        36.00 
TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 
        1.02        15.02         4.01        69.04        12.66        20.91 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       20.55        18.84        18.54        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV 
       15.98        12.79        14.66        21.14        16.44        11.24 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C 
       11.31        22.29        19.96         7.99        72.23        11.38 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 
       17.06         0.56         6.21        63.06         1.51         5.92 
TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       18.15        11.77         6.58        21.17        33.40        36.36 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT 
       18.81        18.38        12.46         6.74         6.51        10.62 
TCGA-IN-AB1V TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       15.75        37.64        36.95        14.04        45.67         8.52 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        6.08         9.24         8.61         5.13        16.67        37.91 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        8.94         5.79        13.25        18.48        43.36        37.41 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
        7.73        22.19        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       14.33        18.74        20.81         1.71        42.64         9.50 
TCGA-VQ-A91Y TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        9.73        21.04        42.54        11.24        18.41        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       38.93        27.55        12.43         0.79 

$`9P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        26.70        11.70        19.56         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.87        17.29        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       30.90        44.94        21.90        36.16        35.84        33.63 
TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8078 
       15.32         9.07        29.56        33.21        14.43        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
        0.26         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 
       31.27        14.79         7.36        25.05         3.72         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8690 TCGA-BR-A44T 
       26.73        24.79        31.96        32.58        10.68        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        7.53         6.08        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
       14.17         0.53        28.34        32.52         0.46        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
       21.44        16.14         5.13        13.41        13.18        13.35 
TCGA-CD-5804 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 
       12.10        12.33        12.30        12.39        12.59        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
       12.43        12.30        11.31        12.43         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
        7.99         8.05        14.01         0.00         9.01         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       30.97         6.97         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       12.03        28.96        65.10        21.07         7.99        25.71 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 
       19.13        18.61        17.85        15.22        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.44        20.32        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.13         0.62        14.47        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       14.07        22.29        59.54         5.03        13.58         5.52 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 
       77.29        52.21        30.51        26.47        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN 
       14.07        15.68         3.45         3.39        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.44        12.59        11.70        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 
       63.62         3.72        19.73        18.21        74.53         4.60 
TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44        35.61        16.87        19.04         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
        5.46        13.02        21.73        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       34.29        46.26        16.31         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        29.59        64.57        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Z 
       11.70        21.83        61.22        32.88        60.85        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       66.81         2.66        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       26.04        16.14        17.26 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.56              0.00 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            72.23            122.30 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           13.775            15.650 
[1] "0.6 - 72.2 (13.8)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1.2"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         1        7       10       15        11        18
  9P LOSS WILD-TYPE       1        9       31       17        29        38
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           1         25         22         12       18
  9P LOSS WILD-TYPE         2         56         41         27       26
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 7                 9
  STAGE IB                10                31
  STAGE II                15                17
  STAGE IIA               11                29
  STAGE IIB               18                38
  STAGE III                1                 2
  STAGE IIIA              25                56
  STAGE IIIB              22                41
  STAGE IIIC              12                27
  STAGE IV                18                26
[1] 11  2
[1] 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     8  32  69  36
  9P LOSS WILD-TYPE  15  61 127  83
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               8                15
  T2              32                61
  T3              69               127
  T4              36                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9P LOSS MUTATED   39 40 36 28
  9P LOSS WILD-TYPE 91 79 50 60
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              39                91
  N1              40                79
  N2              36                50
  N3              28                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   133   9
  9P LOSS WILD-TYPE 256  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    133    9
  9P LOSS WILD-TYPE  256   21
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             133               256
  1               9                21
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    56  93
  9P LOSS WILD-TYPE 102 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     56   93
  9P LOSS WILD-TYPE  102  190
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              56               102
  MALE                93               190
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   108  27
  9P LOSS WILD-TYPE 214  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    108   27
  9P LOSS WILD-TYPE  214   49
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              108               214
  YES              27                49
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  9P LOSS MUTATED                                          3
  9P LOSS WILD-TYPE                                       10
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  9P LOSS MUTATED                                      14
  9P LOSS WILD-TYPE                                    58
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                       54
  9P LOSS WILD-TYPE                                                    109
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  9P LOSS MUTATED                                                   6
  9P LOSS WILD-TYPE                                                15
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                                  35
  9P LOSS WILD-TYPE                                                                47
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  9P LOSS MUTATED                                                    3
  9P LOSS WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  9P LOSS MUTATED                                                 33
  9P LOSS WILD-TYPE                                               46
D58V9, multiclass
                                                                   clus
vv                                                                  9P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          14
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         54
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               33
                                                                   clus
vv                                                                  9P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            58
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          109
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                47
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 46
[1] 7 2
[1] TRUE
[1] "dimension of 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   120   5   6   5
  9P LOSS WILD-TYPE 229  13  13  20
D58V10, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             120               229
  R1               5                13
  R2               6                13
  RX               5                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"
D58V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9P LOSS MUTATED      27                         6
  9P LOSS WILD-TYPE    61                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           1    94
  9P LOSS WILD-TYPE                                         0   184
D58V12, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                                  27                61
  BLACK OR AFRICAN AMERICAN                               6                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  94               184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2 102
  9P LOSS WILD-TYPE   3 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2  102
  9P LOSS WILD-TYPE    3  214
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             102               214
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    53  45
  9Q LOSS WILD-TYPE 193 124
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               98               317 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               45               124 
$`9Q LOSS MUTATED`
TCGA-VQ-A94U TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6803 
       26.93         4.08         9.67        13.68        19.33        31.20 
TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 
        9.21        39.78        28.73         3.45        37.25        11.44 
TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       19.96        22.19        17.52         5.39        25.18         9.21 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44U TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 
        9.86        20.88        13.87         1.48         0.72        13.51 
TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
        1.15        13.02        11.21        12.76        12.59         7.17 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A48C TCGA-CD-A4MH 
       11.64        15.39        12.07         6.31        11.61        12.20 
TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4455 TCGA-D7-6519 
        3.02        54.08         4.01        29.98        12.03        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.84        18.54        13.35        10.26        15.98        12.79 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-D7-A74A 
       18.21        14.66        21.14        16.44        22.29        19.96 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
        7.99        72.23        11.38        17.06        13.58         0.56 
TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4HD 
       63.06         5.92        11.77         6.58         2.10        33.40 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93H 
       18.38        12.46         6.74         6.51        15.75        37.64 
TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A7C1 
       36.95        14.04        45.67         8.52         6.08        16.67 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       37.91         8.94         5.79        13.25        18.48        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS 
       37.41        22.19        12.79         2.70        17.85        13.35 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 
       20.81         1.71         9.73        21.04        42.54        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6J 
       38.93        27.55 

$`9Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       20.15         9.86        27.35        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        4.64         7.43        18.35        30.90         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       17.29        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90        36.16        35.24        35.84        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       18.15        15.32         9.07        29.56        33.21        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        13.08         0.26         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.05         3.72        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 
       31.96        32.58         8.22        10.68        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        34.98        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42        21.44        16.14         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8528 
       13.15        13.18        13.35        12.10        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       12.30        12.39        12.59        12.82        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        12.43         6.58        11.77        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
       27.02        15.95         1.02         7.99         8.05        14.01 
TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       19.07         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 
       20.91        19.13        18.61        17.85        17.19        15.22 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       17.19        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
       15.65         8.38         4.34         7.13         0.62        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       21.27         3.48        19.53        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
        5.03         5.52         6.21        77.29        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL 
       15.68        36.36         3.45        18.81         3.39        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
       19.53         6.44        12.59        10.62        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE 
        2.53         5.56        63.62         3.72        19.73        18.21 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       74.53         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        16.87        19.04         0.92        48.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       13.02        21.73        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO 
       34.29        46.26        16.31         2.50         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       42.64        60.85         9.50        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        66.81         2.66 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       11.24        18.41        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        12.43        17.26         0.79 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.56              0.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            72.23            122.30 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            13.63             15.58 
[1] "0.6 - 72.2 (13.6)"  "0.0 - 122.3 (15.6)"
[1] "hr=" "1.3"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         1        5        6       11         9        12
  9Q LOSS WILD-TYPE       1       11       35       21        31        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           1         18         15         10       10
  9Q LOSS WILD-TYPE         2         63         48         29       34
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 5                11
  STAGE IB                 6                35
  STAGE II                11                21
  STAGE IIA                9                31
  STAGE IIB               12                44
  STAGE III                1                 2
  STAGE IIIA              18                63
  STAGE IIIB              15                48
  STAGE IIIC              10                29
  STAGE IV                10                34
[1] 11  2
[1] 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     5  22  51  23
  9Q LOSS WILD-TYPE  18  71 145  96
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               5                18
  T2              22                71
  T3              51               145
  T4              23                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q LOSS MUTATED    27  28  23  22
  9Q LOSS WILD-TYPE 103  91  63  66
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              27               103
  N1              28                91
  N2              23                63
  N3              22                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    91   7
  9Q LOSS WILD-TYPE 298  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     91    7
  9Q LOSS WILD-TYPE  298   23
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              91               298
  1               7                23
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    34  70
  9Q LOSS WILD-TYPE 124 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     34   70
  9Q LOSS WILD-TYPE  124  213
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              34               124
  MALE                70               213
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    75  19
  9Q LOSS WILD-TYPE 247  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     75   19
  9Q LOSS WILD-TYPE  247   57
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               75               247
  YES              19                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  9Q LOSS MUTATED                                          1
  9Q LOSS WILD-TYPE                                       12
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  9Q LOSS MUTATED                                      12
  9Q LOSS WILD-TYPE                                    60
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                       40
  9Q LOSS WILD-TYPE                                                    123
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  9Q LOSS MUTATED                                                   4
  9Q LOSS WILD-TYPE                                                17
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                                  22
  9Q LOSS WILD-TYPE                                                                60
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  9Q LOSS MUTATED                                                    1
  9Q LOSS WILD-TYPE                                                  7
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  9Q LOSS MUTATED                                                 24
  9Q LOSS WILD-TYPE                                               55
D59V9, multiclass
                                                                   clus
vv                                                                  9Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         40
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              22
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               24
                                                                   clus
vv                                                                  9Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          123
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 55
[1] 7 2
[1] TRUE
[1] "dimension of 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    83   3   4   4
  9Q LOSS WILD-TYPE 266  15  15  21
D59V10, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              83               266
  R1               3                15
  R2               4                15
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9Q LOSS MUTATED      23                         6
  9Q LOSS WILD-TYPE    65                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           0    65
  9Q LOSS WILD-TYPE                                         1   213
D59V12, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                                  23                65
  BLACK OR AFRICAN AMERICAN                               6                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  65               213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1  75
  9Q LOSS WILD-TYPE   4 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   75
  9Q LOSS WILD-TYPE    4  241
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              75               241
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    30  30
  10P LOSS WILD-TYPE 216 139
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                60                355 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                30                139 
$`10P LOSS MUTATED`
TCGA-CG-4475 TCGA-FP-A8CX TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-4267 
       22.98         0.23        19.56        18.35         9.67         6.18 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8291 
       19.33        26.10        35.24         3.45        11.44        19.96 
TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4IY TCGA-CD-8525 TCGA-CD-8528 
       17.52        20.22         7.53        12.89        12.59        12.33 
TCGA-CD-8533 TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6527 
       15.39         7.99        12.03        69.04        18.54        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EV TCGA-EQ-8122 
       15.22        15.98        11.31        18.21        11.24         7.99 
TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8249 TCGA-IN-8462 
       19.53         0.56         5.52        63.06        28.96        18.81 
TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RR TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-RD-A8N1 
       18.38         6.44         6.74        45.67         8.52       115.69 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        8.94         5.79        48.79        13.02        18.48        43.36 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q 
       22.19        17.85        13.35        39.45        18.74        20.81 
TCGA-VQ-A928 TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-ZQ-A9CR 
        5.72        11.24        18.41        43.66        16.14         0.79 

$`10P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
       47.05        21.99        79.07        16.24        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
       27.35        26.93        58.03        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         4.08         9.34         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        29.42         2.66         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        6.18        31.10        13.08         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        34.98         1.48        27.55        28.57         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.35        11.21        12.10        12.76        12.53         7.17 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        19.07         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        20.91        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
       17.85        13.35        17.19        12.79        12.36        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM 
       22.29        17.06        59.54         5.03        13.58         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ 
       15.68        33.40        36.36         3.45         3.39        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       13.35        19.53        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       15.75        13.51         2.53         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZI 
       36.95         3.72        19.73        14.04        18.21        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU 
       57.44        35.61        16.87        19.04         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.70         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        73.41        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        21.04         2.66        42.54        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        17.13        54.12        26.04        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.23               0.00 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            115.69             122.30 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             16.06              14.47 
[1] "0.2 - 115.7 (16.1)" "0.0 - 122.3 (14.5)"
[1] "hr=" "1.3"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         1        2        3        4         1        12
  10P LOSS WILD-TYPE       1       14       38       28        39        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           0         13          9          6        8
  10P LOSS WILD-TYPE         3         68         54         33       36
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  2                 14
  STAGE IB                  3                 38
  STAGE II                  4                 28
  STAGE IIA                 1                 39
  STAGE IIB                12                 44
  STAGE III                 0                  3
  STAGE IIIA               13                 68
  STAGE IIIB                9                 54
  STAGE IIIC                6                 33
  STAGE IV                  8                 36
[1] 11  2
[1] 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     4  14  31  11
  10P LOSS WILD-TYPE  19  79 165 108
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                4                 19
  T2               14                 79
  T3               31                165
  T4               11                108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P LOSS MUTATED    11  17  16  17
  10P LOSS WILD-TYPE 119 102  70  71
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               11                119
  N1               17                102
  N2               16                 70
  N3               17                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    57   3
  10P LOSS WILD-TYPE 332  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     57    3
  10P LOSS WILD-TYPE  332   27
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               57                332
  1                3                 27
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    20  44
  10P LOSS WILD-TYPE 138 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     20   44
  10P LOSS WILD-TYPE  138  239
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               20                138
  MALE                 44                239
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    44  16
  10P LOSS WILD-TYPE 278  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     44   16
  10P LOSS WILD-TYPE  278   60
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                44                278
  YES               16                 60
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  10P LOSS MUTATED                                          3
  10P LOSS WILD-TYPE                                       10
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  10P LOSS MUTATED                                       6
  10P LOSS WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                       20
  10P LOSS WILD-TYPE                                                    143
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  10P LOSS MUTATED                                                   6
  10P LOSS WILD-TYPE                                                15
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                                  12
  10P LOSS WILD-TYPE                                                                70
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  10P LOSS MUTATED                                                    2
  10P LOSS WILD-TYPE                                                  6
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  10P LOSS MUTATED                                                 14
  10P LOSS WILD-TYPE                                               65
D60V9, multiclass
                                                                   clus
vv                                                                  10P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                14
                                                                   clus
vv                                                                  10P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  65
[1] 7 2
[1] TRUE
[1] "dimension of 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    51   3   1   5
  10P LOSS WILD-TYPE 298  15  18  20
D60V10, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               51                298
  R1                3                 15
  R2                1                 18
  RX                5                 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"
D60V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10P LOSS MUTATED       8                         3
  10P LOSS WILD-TYPE    80                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           0    44
  10P LOSS WILD-TYPE                                         1   234
D60V12, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                                    8                 80
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   44                234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  43
  10P LOSS WILD-TYPE   4 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   43
  10P LOSS WILD-TYPE    4  273
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               43                273
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    38  26
  10Q LOSS WILD-TYPE 208 143
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                64                351 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                26                143 
$`10Q LOSS MUTATED`
TCGA-CG-4475 TCGA-FP-A8CX TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6458 
       22.98         0.23        19.56        18.35         9.67        19.33 
TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8483 
       35.24         3.45        11.44        19.96        17.52         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A4CQ TCGA-CD-5799 TCGA-CD-8525 
        9.21        20.22         9.86        34.98        13.02        12.59 
TCGA-CD-8528 TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4455 TCGA-CG-4466 
       12.33        12.43         7.99         4.01        12.03        18.97 
TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        4.01        19.13        18.54        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 
       12.79         7.99        19.53         0.56         5.52         5.92 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GH TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI 
       28.96        22.82        11.77        33.40        18.81        18.38 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF 
        6.44         6.74         6.51        37.64        45.67         8.52 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94         5.79        48.79         5.46        13.02        18.48 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A94O 
       22.19        17.85        39.45        18.74         9.50        21.04 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       11.24        43.66        38.93         0.79 

$`10Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
       47.05        21.99        79.07        16.24        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
       27.35        26.93        58.03        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       32.25         8.05         0.56        29.42         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       16.14         5.13        13.41        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       11.21        12.10        12.76        12.53         7.17        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        12.30        11.31        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         8.05        54.08        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       19.07         0.00         9.01         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
      105.07        12.03        15.02        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       21.07         7.99        25.71        12.66        20.91        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 
       18.84        18.61        17.85        13.35        17.19        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         0.62        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       59.54         5.03        13.58         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         1.51        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
       21.17        14.07        15.68        36.36         3.45         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       12.46        13.35        19.53        12.59        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73        14.04        18.21        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV 
       57.44        35.61        16.87        19.04         0.92        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        14.33        73.41        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 
        6.58         5.72        66.81         2.66        42.54        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.23               0.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             48.79             122.30 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             13.02              15.02 
[1] "0.2 - 48.8 (13.0)"  "0.0 - 122.3 (15.0)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         1        3        3        4         3        10
  10Q LOSS WILD-TYPE       1       13       38       28        37        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           0         15          7         10        7
  10Q LOSS WILD-TYPE         3         66         56         29       37
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  3                 13
  STAGE IB                  3                 38
  STAGE II                  4                 28
  STAGE IIA                 3                 37
  STAGE IIB                10                 46
  STAGE III                 0                  3
  STAGE IIIA               15                 66
  STAGE IIIB                7                 56
  STAGE IIIC               10                 29
  STAGE IV                  7                 37
[1] 11  2
[1] 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     5  14  30  15
  10Q LOSS WILD-TYPE  18  79 166 104
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                5                 18
  T2               14                 79
  T3               30                166
  T4               15                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"
                    vv
clus                  N0  N1  N2  N3
  10Q LOSS MUTATED    12  18  15  20
  10Q LOSS WILD-TYPE 118 101  71  68
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               12                118
  N1               18                101
  N2               15                 71
  N3               20                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    58   6
  10Q LOSS WILD-TYPE 331  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     58    6
  10Q LOSS WILD-TYPE  331   24
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               58                331
  1                6                 24
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    24  44
  10Q LOSS WILD-TYPE 134 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     24   44
  10Q LOSS WILD-TYPE  134  239
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               24                134
  MALE                 44                239
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    48  14
  10Q LOSS WILD-TYPE 274  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     48   14
  10Q LOSS WILD-TYPE  274   62
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                48                274
  YES               14                 62
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  10Q LOSS MUTATED                                          3
  10Q LOSS WILD-TYPE                                       10
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  10Q LOSS MUTATED                                       5
  10Q LOSS WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                       20
  10Q LOSS WILD-TYPE                                                    143
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  10Q LOSS MUTATED                                                   5
  10Q LOSS WILD-TYPE                                                16
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                                  16
  10Q LOSS WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  10Q LOSS MUTATED                                                    1
  10Q LOSS WILD-TYPE                                                  7
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  10Q LOSS MUTATED                                                 17
  10Q LOSS WILD-TYPE                                               62
D61V9, multiclass
                                                                   clus
vv                                                                  10Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               16
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                17
                                                                   clus
vv                                                                  10Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  62
[1] 7 2
[1] TRUE
[1] "dimension of 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    53   2   3   4
  10Q LOSS WILD-TYPE 296  16  16  21
D61V10, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               53                296
  R1                2                 16
  R2                3                 16
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10Q LOSS MUTATED      12                         4
  10Q LOSS WILD-TYPE    76                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           0    43
  10Q LOSS WILD-TYPE                                         1   235
D61V12, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                                   12                 76
  BLACK OR AFRICAN AMERICAN                                4                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   43                235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  47
  10Q LOSS WILD-TYPE   4 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   47
  10Q LOSS WILD-TYPE    4  269
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               47                269
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    32  31
  11P LOSS WILD-TYPE 214 138
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                352 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                31                138 
$`11P LOSS MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-VQ-A8PU TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4279 
       47.05        21.99        27.35         6.61         6.97         9.57 
TCGA-BR-6564 TCGA-BR-7723 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-A4CS 
       26.10        28.73         9.60         2.66         7.40         1.48 
TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-A486 
        0.72        13.02        13.15        13.35         7.17         6.31 
TCGA-CD-A48A TCGA-CG-4443 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5578 
       12.43        29.98        30.97        12.03         4.01        12.66 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       20.91        20.55        18.54        10.26        15.22        15.98 
TCGA-D7-8578 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-A72C TCGA-FP-8211 TCGA-HJ-7597 
       21.14        19.96         0.62        11.38        13.58        26.47 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 
       18.15        28.96        22.75         2.10        23.84        23.80 
TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-R5-A7O7 
       21.17         3.39        13.35         6.44         6.74        45.67 
TCGA-R5-A7ZE TCGA-RD-A8MW TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8PK 
       18.21        37.91        48.79        13.25        37.41        17.85 
TCGA-VQ-A8PS TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O 
       13.35        18.74        55.56         9.04         4.54        21.04 
TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6K 
       42.54        43.66        12.43 

$`11P LOSS WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       26.93        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         9.44         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 
        4.08         4.08         9.34         9.67         6.18         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56        29.42        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       15.58         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       12.07        12.82        12.43        12.30        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        12.00         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 
       65.10        69.04        21.07         7.99        25.71        19.13 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 
       18.84        18.61        17.85        13.35        17.19        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        14.66        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        4.34         7.13         7.99        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       52.21        30.51         1.51         5.92        24.39        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        0.26        12.95        29.00        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       36.36         3.45        18.81        18.38        12.46        19.53 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
        2.53         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       19.73        14.04         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       35.61        16.87        19.04         5.79         0.92         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        18.48        43.36        21.73        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        21.83        61.22        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 
       42.64        60.85         9.50         9.73         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58         5.72        66.81         2.66        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        17.26         0.79 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.62               0.00 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             55.56             122.30 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            15.220             14.775 
[1] "0.6 - 55.6 (15.2)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.3"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         0        1        6        6         4         5
  11P LOSS WILD-TYPE       2       15       35       26        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           0         17          4          8        9
  11P LOSS WILD-TYPE         3         64         59         31       35
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 15
  STAGE IB                  6                 35
  STAGE II                  6                 26
  STAGE IIA                 4                 36
  STAGE IIB                 5                 51
  STAGE III                 0                  3
  STAGE IIIA               17                 64
  STAGE IIIB                4                 59
  STAGE IIIC                8                 31
  STAGE IV                  9                 35
[1] 11  2
[1] 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     2  19  28  15
  11P LOSS WILD-TYPE  21  74 168 104
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                2                 21
  T2               19                 74
  T3               28                168
  T4               15                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"
                    vv
clus                  N0  N1  N2  N3
  11P LOSS MUTATED    13  20  15  15
  11P LOSS WILD-TYPE 117  99  71  73
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               13                117
  N1               20                 99
  N2               15                 71
  N3               15                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    54   7
  11P LOSS WILD-TYPE 335  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     54    7
  11P LOSS WILD-TYPE  335   23
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               54                335
  1                7                 23
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    21  43
  11P LOSS WILD-TYPE 137 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     21   43
  11P LOSS WILD-TYPE  137  240
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               21                137
  MALE                 43                240
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    46  14
  11P LOSS WILD-TYPE 276  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     46   14
  11P LOSS WILD-TYPE  276   62
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                46                276
  YES               14                 62
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  11P LOSS MUTATED                                          2
  11P LOSS WILD-TYPE                                       11
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  11P LOSS MUTATED                                       7
  11P LOSS WILD-TYPE                                    65
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                       16
  11P LOSS WILD-TYPE                                                    147
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  11P LOSS MUTATED                                                   2
  11P LOSS WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                                  15
  11P LOSS WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  11P LOSS MUTATED                                                    4
  11P LOSS WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  11P LOSS MUTATED                                                 18
  11P LOSS WILD-TYPE                                               61
D62V9, multiclass
                                                                   clus
vv                                                                  11P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               15
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                18
                                                                   clus
vv                                                                  11P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of 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    46   3   5   4
  11P LOSS WILD-TYPE 303  15  14  21
D62V10, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               46                303
  R1                3                 15
  R2                5                 14
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11P LOSS MUTATED      15                         1
  11P LOSS WILD-TYPE    73                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           0    39
  11P LOSS WILD-TYPE                                         1   239
D62V12, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                1                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   39                239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     1  43
  11P LOSS WILD-TYPE   4 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1   43
  11P LOSS WILD-TYPE    4  273
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               43                273
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    30  30
  11Q LOSS WILD-TYPE 216 139
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                60                355 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                30                139 
$`11Q LOSS MUTATED`
TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4279 TCGA-BR-6709 
        0.23        27.35         6.61         6.97         9.57        12.16 
TCGA-BR-7723 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-A4CQ 
       28.73         9.60         2.66        17.52        20.22        34.98 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 
        1.48         0.72        13.51         1.15        13.02        13.15 
TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-A48A TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4455 
       13.35         7.17        12.43         8.05        29.98        12.03 
TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6815 
       12.03        12.66        20.91        18.54        10.26        15.98 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-7916 TCGA-FP-8211 TCGA-HJ-7597 TCGA-HU-8249 
       19.96         0.62        14.07        13.58        26.47        28.96 
TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-A6RL 
        0.76        22.75         2.10        23.84        21.17        13.35 
TCGA-IN-A6RP TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A805 TCGA-RD-A8MW 
        6.44        14.04        45.67        18.21         9.24        37.91 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91Q 
       48.79        13.25        37.41        17.85        13.35        20.81 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6K 
       55.56         9.04        21.04        42.54        11.24        12.43 

$`11Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.86        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.01         9.47         9.44         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       33.63        39.78        18.15        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
       29.59        32.25         8.05         0.56        29.42        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18         9.21         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
       10.68        34.13        13.87         7.53         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
        0.66        32.52         0.46        20.65        20.42        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 
       16.14         5.13        13.41        13.18        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        12.30        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 
        1.02         7.99        54.08         4.01        14.01        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        25.71        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 
       18.61        17.85        13.35        17.19        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34         7.13         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        19.53        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       18.15        22.32        22.82        21.07        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68        24.20         3.25        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 
       20.25         0.26        12.95        29.00        23.80        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       18.38        12.46        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF 
       63.62        37.64        36.95         3.72        19.73         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       74.53         6.08         4.60        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       57.44         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92         5.46        13.02        18.48        43.36        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       16.31        22.19         2.50        12.79         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        9.27        23.41        15.65        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        2.66        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       17.13        54.12        26.04        16.14        27.55        17.26 
TCGA-ZQ-A9CR 
        0.79 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.23               0.00 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             55.56             122.30 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             13.35              15.58 
[1] "0.2 - 55.6 (13.3)"  "0.0 - 122.3 (15.6)"
[1] "hr=" "1.4"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         0        3        2        8         3         4
  11Q LOSS WILD-TYPE       2       13       39       24        37        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           0         14          9          8        7
  11Q LOSS WILD-TYPE         3         67         54         31       37
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 13
  STAGE IB                  2                 39
  STAGE II                  8                 24
  STAGE IIA                 3                 37
  STAGE IIB                 4                 52
  STAGE III                 0                  3
  STAGE IIIA               14                 67
  STAGE IIIB                9                 54
  STAGE IIIC                8                 31
  STAGE IV                  7                 37
[1] 11  2
[1] 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     4  14  28  15
  11Q LOSS WILD-TYPE  19  79 168 104
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                4                 19
  T2               14                 79
  T3               28                168
  T4               15                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"
                    vv
clus                  N0  N1  N2  N3
  11Q LOSS MUTATED     9  19  14  17
  11Q LOSS WILD-TYPE 121 100  72  71
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                9                121
  N1               19                100
  N2               14                 72
  N3               17                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    50   5
  11Q LOSS WILD-TYPE 339  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     50    5
  11Q LOSS WILD-TYPE  339   25
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               50                339
  1                5                 25
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    17  44
  11Q LOSS WILD-TYPE 141 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     17   44
  11Q LOSS WILD-TYPE  141  239
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               17                141
  MALE                 44                239
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    45  11
  11Q LOSS WILD-TYPE 277  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     45   11
  11Q LOSS WILD-TYPE  277   65
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                45                277
  YES               11                 65
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  11Q LOSS MUTATED                                          3
  11Q LOSS WILD-TYPE                                       10
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  11Q LOSS MUTATED                                       5
  11Q LOSS WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                       19
  11Q LOSS WILD-TYPE                                                    144
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  11Q LOSS MUTATED                                                   3
  11Q LOSS WILD-TYPE                                                18
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                                  13
  11Q LOSS WILD-TYPE                                                                69
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  11Q LOSS MUTATED                                                    2
  11Q LOSS WILD-TYPE                                                  6
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  11Q LOSS MUTATED                                                 16
  11Q LOSS WILD-TYPE                                               63
D63V9, multiclass
                                                                   clus
vv                                                                  11Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               13
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                16
                                                                   clus
vv                                                                  11Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 69
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  63
[1] 7 2
[1] TRUE
[1] "dimension of 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    43   4   2   4
  11Q LOSS WILD-TYPE 306  14  17  21
D63V10, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               43                306
  R1                4                 14
  R2                2                 17
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11Q LOSS MUTATED      13                         1
  11Q LOSS WILD-TYPE    75                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           0    39
  11Q LOSS WILD-TYPE                                         1   239
D63V12, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                                   13                 75
  BLACK OR AFRICAN AMERICAN                                1                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   39                239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  43
  11Q LOSS WILD-TYPE   4 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   43
  11Q LOSS WILD-TYPE    4  273
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               43                273
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    27  32
  12P LOSS WILD-TYPE 219 137
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                59                356 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                32                137 
$`12P LOSS MUTATED`
TCGA-VQ-A8PU TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 
       27.35         6.61         4.08         9.67         6.18        17.29 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8483 TCGA-BR-8485 
       35.24        33.63         3.45        11.44         5.39         9.21 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4J6 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8527 
        9.86         8.22         0.66        13.15        13.35         7.17 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4443 
       12.82         6.31        11.31        12.20         7.99        29.98 
TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A4YT 
       30.97        15.02        69.04        15.22        12.33        14.27 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8631 TCGA-HU-8245 TCGA-HU-A4GH 
        0.62         7.99        72.23         0.56        18.15        11.77 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-KB-A93J 
       12.95        23.84        23.80        13.35        19.53        36.95 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       14.04        45.67         5.46        13.02        12.79         2.70 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A925 
       13.35        14.33         9.50        55.56         2.01         4.54 
TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       21.04        11.24        43.66        16.14         0.79 

$`12P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       20.15         9.86        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 
        7.43        18.35        30.90         4.08         9.34         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       44.94        21.90         9.21        36.16        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72        25.18        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       31.96        32.58        20.88        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
       21.44        16.14         5.13        13.41        13.02        13.18 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       11.21        12.10        12.76        12.59        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       12.43        12.30        12.43        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08         4.01        14.01        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       12.03        28.96        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 
        8.38         4.34        19.96         7.13        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26         2.10        29.00 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81         3.39        18.38        12.46         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        37.64         3.72        19.73 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       22.19         2.50        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        29.59        64.57        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       21.83        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
       42.64        60.85         9.73         9.04        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 
        5.72        66.81         2.66        42.54        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       38.93        32.94        17.13        54.12        26.04        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.56               0.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             72.23             122.30 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            12.820             15.965 
[1] "0.6 - 72.2 (12.8)"  "0.0 - 122.3 (16.0)"
[1] "hr=" "1.7"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         0        3        8        5         8         5
  12P LOSS WILD-TYPE       2       13       33       27        32        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           0         13          7          6        5
  12P LOSS WILD-TYPE         3         68         56         33       39
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 13
  STAGE IB                  8                 33
  STAGE II                  5                 27
  STAGE IIA                 8                 32
  STAGE IIB                 5                 51
  STAGE III                 0                  3
  STAGE IIIA               13                 68
  STAGE IIIB                7                 56
  STAGE IIIC                6                 33
  STAGE IV                  5                 39
[1] 11  2
[1] 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     3  17  29  11
  12P LOSS WILD-TYPE  20  76 167 108
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                3                 20
  T2               17                 76
  T3               29                167
  T4               11                108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P LOSS MUTATED    20  14  13  12
  12P LOSS WILD-TYPE 110 105  73  76
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               20                110
  N1               14                105
  N2               13                 73
  N3               12                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    53   4
  12P LOSS WILD-TYPE 336  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     53    4
  12P LOSS WILD-TYPE  336   26
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               53                336
  1                4                 26
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    25  37
  12P LOSS WILD-TYPE 133 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     25   37
  12P LOSS WILD-TYPE  133  246
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               25                133
  MALE                 37                246
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    48  10
  12P LOSS WILD-TYPE 274  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     48   10
  12P LOSS WILD-TYPE  274   66
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                48                274
  YES               10                 66
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  12P LOSS MUTATED                                          1
  12P LOSS WILD-TYPE                                       12
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  12P LOSS MUTATED                                       4
  12P LOSS WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                       23
  12P LOSS WILD-TYPE                                                    140
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  12P LOSS MUTATED                                                   0
  12P LOSS WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                                  13
  12P LOSS WILD-TYPE                                                                69
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  12P LOSS MUTATED                                                    3
  12P LOSS WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  12P LOSS MUTATED                                                 18
  12P LOSS WILD-TYPE                                               61
D64V9, multiclass
                                                                   clus
vv                                                                  12P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               13
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                18
                                                                   clus
vv                                                                  12P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           140
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 69
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of 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    44   2   4   5
  12P LOSS WILD-TYPE 305  16  15  20
D64V10, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               44                305
  R1                2                 16
  R2                4                 15
  RX                5                 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"
D64V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12P LOSS MUTATED      13                         3
  12P LOSS WILD-TYPE    75                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           0    37
  12P LOSS WILD-TYPE                                         1   241
D64V12, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                                   13                 75
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   37                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  38
  12P LOSS WILD-TYPE   4 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   38
  12P LOSS WILD-TYPE    4  278
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               38                278
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    22  26
  12Q LOSS WILD-TYPE 224 143
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                48                367 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                26                143 
$`12Q LOSS MUTATED`
TCGA-VQ-A8PU TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 
       27.35         6.61         9.67        17.29        35.24        33.63 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8683 
        3.45        11.44        29.42         5.39         9.21         9.86 
TCGA-BR-8687 TCGA-BR-A4J6 TCGA-CD-5802 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 
        8.22         0.66        13.35        11.31        12.20        20.02 
TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6528 TCGA-D7-A6F2 
        7.99        29.98        15.02        69.04        15.22        15.65 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-A4GH TCGA-HU-A4H2 
        0.62         7.99        13.58         0.56        11.77        12.95 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-VQ-A8DU 
       19.53         6.44        37.64        45.67        18.21         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91Z TCGA-VQ-A925 
       18.48        12.79        17.85        13.35        55.56         4.54 
TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       21.04        11.24        43.66        16.14        12.43         0.79 

$`12Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       20.15         9.86        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       35.84        39.78        18.15        15.32        28.73         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        14.43         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
        9.60        32.25         8.05         0.56         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       25.05         3.72        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        31.96        32.58        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        12.43        11.61         6.58        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34        19.96         7.13        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       17.06        59.54         5.03         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       12.46        13.35         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       36.95         3.72        19.73        14.04         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.25        13.02        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       34.29        46.26        16.31        22.19         2.50         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.50         9.73         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 
        5.72        66.81         2.66        42.54        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       38.93        32.94        17.13        54.12        26.04        27.55 
TCGA-ZA-A8F6 
       17.26 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.56               0.00 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             69.04             122.30 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             13.15              15.58 
[1] "0.6 - 69.0 (13.1)"  "0.0 - 122.3 (15.6)"
[1] "hr=" "1.6"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         0        2        5        3         6         6
  12Q LOSS WILD-TYPE       2       14       36       29        34        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0         10          7          8        3
  12Q LOSS WILD-TYPE         3         71         56         31       41
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 14
  STAGE IB                  5                 36
  STAGE II                  3                 29
  STAGE IIA                 6                 34
  STAGE IIB                 6                 50
  STAGE III                 0                  3
  STAGE IIIA               10                 71
  STAGE IIIB                7                 56
  STAGE IIIC                8                 31
  STAGE IV                  3                 41
[1] 11  2
[1] 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     4   7  29  10
  12Q LOSS WILD-TYPE  19  86 167 109
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                4                 19
  T2                7                 86
  T3               29                167
  T4               10                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q LOSS MUTATED    15  10  12  13
  12Q LOSS WILD-TYPE 115 109  74  75
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               15                115
  N1               10                109
  N2               12                 74
  N3               13                 75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    45   2
  12Q LOSS WILD-TYPE 344  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     45    2
  12Q LOSS WILD-TYPE  344   28
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               45                344
  1                2                 28
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    21  31
  12Q LOSS WILD-TYPE 137 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     21   31
  12Q LOSS WILD-TYPE  137  252
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               21                137
  MALE                 31                252
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    35  11
  12Q LOSS WILD-TYPE 287  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     35   11
  12Q LOSS WILD-TYPE  287   65
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                35                287
  YES               11                 65
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  12Q LOSS MUTATED                                          1
  12Q LOSS WILD-TYPE                                       12
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  12Q LOSS MUTATED                                       3
  12Q LOSS WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                       21
  12Q LOSS WILD-TYPE                                                    142
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  12Q LOSS MUTATED                                                   0
  12Q LOSS WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                                  12
  12Q LOSS WILD-TYPE                                                                70
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  12Q LOSS MUTATED                                                    0
  12Q LOSS WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  12Q LOSS MUTATED                                                 15
  12Q LOSS WILD-TYPE                                               64
D65V9, multiclass
                                                                   clus
vv                                                                  12Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          21
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                15
                                                                   clus
vv                                                                  12Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  64
[1] 7 2
[1] TRUE
[1] "dimension of 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    37   4   2   3
  12Q LOSS WILD-TYPE 312  14  17  22
D65V10, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               37                312
  R1                4                 14
  R2                2                 17
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12Q LOSS MUTATED       7                         2
  12Q LOSS WILD-TYPE    81                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0    35
  12Q LOSS WILD-TYPE                                         1   243
D65V12, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                                    7                 81
  BLACK OR AFRICAN AMERICAN                                2                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   35                243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  30
  12Q LOSS WILD-TYPE   4 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   30
  12Q LOSS WILD-TYPE    4  286
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               30                286
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    20  15
  13Q LOSS WILD-TYPE 226 154
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                35                380 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                15                154 
$`13Q LOSS MUTATED`
TCGA-CG-4475 TCGA-3M-AB46 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-6456 
       22.98        58.03         6.61         6.97         4.08        17.29 
TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7716 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8486 
       26.10        12.16        39.78         7.40        31.10        20.22 
TCGA-BR-8683 TCGA-BR-A4IY TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8533 TCGA-CG-4301 
        9.86        12.89        12.10        12.53        15.39         3.02 
TCGA-CG-4466 TCGA-D7-6525 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-FP-7916 
       18.97        13.35        18.21        21.14        16.44        14.07 
TCGA-FP-8211 TCGA-HF-7133 TCGA-HU-A4GC TCGA-HU-A4H2 TCGA-IN-A6RJ TCGA-IN-A6RR 
       13.58        63.06         3.25        12.95        12.46         6.74 
TCGA-RD-A7BS TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A91Z TCGA-VQ-A925 
       11.05         7.73         1.87        55.56         4.54 

$`13Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.86        27.35        26.93        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.01         9.47         9.44         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
        9.21        36.16        35.24        35.84        33.63        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         6.18        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18        13.35        11.21        12.76        12.59 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       20.55        18.84        18.54        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       12.33        24.72        16.80        19.50        17.19        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       19.53        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
        3.39        18.38        13.35        19.53         6.44        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60         9.24         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       17.85         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       60.85         9.50         9.73         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.87               0.00 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             63.06             122.30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             12.95              15.45 
[1] "1.9 - 63.1 (12.9)"  "0.0 - 122.3 (15.4)"
[1] "hr=" "1.2"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         0        2        4        1         1         5
  13Q LOSS WILD-TYPE       2       14       37       31        39        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           0         11          5          3        3
  13Q LOSS WILD-TYPE         3         70         58         36       41
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 14
  STAGE IB                  4                 37
  STAGE II                  1                 31
  STAGE IIA                 1                 39
  STAGE IIB                 5                 51
  STAGE III                 0                  3
  STAGE IIIA               11                 70
  STAGE IIIB                5                 58
  STAGE IIIC                3                 36
  STAGE IV                  3                 41
[1] 11  2
[1] 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     2   7  20   8
  13Q LOSS WILD-TYPE  21  86 176 111
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                2                 21
  T2                7                 86
  T3               20                176
  T4                8                111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q LOSS MUTATED     9  13   7   7
  13Q LOSS WILD-TYPE 121 106  79  81
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                9                121
  N1               13                106
  N2                7                 79
  N3                7                 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"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    31   1
  13Q LOSS WILD-TYPE 358  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     31    1
  13Q LOSS WILD-TYPE  358   29
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               31                358
  1                1                 29
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    15  22
  13Q LOSS WILD-TYPE 143 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     15   22
  13Q LOSS WILD-TYPE  143  261
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               15                143
  MALE                 22                261
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    29   6
  13Q LOSS WILD-TYPE 293  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     29    6
  13Q LOSS WILD-TYPE  293   70
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                29                293
  YES                6                 70
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  13Q LOSS MUTATED                                          1
  13Q LOSS WILD-TYPE                                       12
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  13Q LOSS MUTATED                                       6
  13Q LOSS WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                       18
  13Q LOSS WILD-TYPE                                                    145
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  13Q LOSS MUTATED                                                   1
  13Q LOSS WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                                   3
  13Q LOSS WILD-TYPE                                                                79
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  13Q LOSS MUTATED                                                    0
  13Q LOSS WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  13Q LOSS MUTATED                                                  7
  13Q LOSS WILD-TYPE                                               72
D66V9, multiclass
                                                                   clus
vv                                                                  13Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          18
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 7
                                                                   clus
vv                                                                  13Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 79
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  72
[1] 7 2
[1] TRUE
[1] "dimension of 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    26   3   2   4
  13Q LOSS WILD-TYPE 323  15  17  21
D66V10, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               26                323
  R1                3                 15
  R2                2                 17
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  13Q LOSS MUTATED       8                         0
  13Q LOSS WILD-TYPE    80                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           0    24
  13Q LOSS WILD-TYPE                                         1   254
D66V12, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                                    8                 80
  BLACK OR AFRICAN AMERICAN                                0                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   24                254
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  27
  13Q LOSS WILD-TYPE   4 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   27
  13Q LOSS WILD-TYPE    4  289
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               27                289
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    64  43
  14Q LOSS WILD-TYPE 182 126
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               107                308 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                43                126 
$`14Q LOSS MUTATED`
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       27.35        26.93        19.56        11.01         9.44         6.61 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
        4.08         9.67         9.57        19.33        26.10         9.17 
TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
       12.16        31.20        35.24        33.63        39.78        28.73 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8381 
       33.21        37.25        29.42         2.66        14.79         7.36 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A4CS 
        5.39        25.18         9.21        24.79        20.88         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF 
        0.72         0.66        32.52         0.46        20.65         1.15 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8534 
       13.18        11.21        12.76         7.17        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 
       12.82        11.31        12.20        20.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4477 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 
       54.08        30.97        20.55        18.84        18.54        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 
       10.26        15.98        14.66        16.44        11.31        22.29 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 
       19.96         7.99        11.38        14.07        17.06         0.56 
TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GP 
       26.47        18.15        28.96         3.25        11.77         8.98 
TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RP 
        2.10        23.84        33.40        36.36        13.35         6.44 
TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A666 TCGA-RD-A7C1 
        6.74        11.70         2.53        37.64        14.04        16.67 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       37.91       115.69         8.94         5.46        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       43.36         7.73        46.26        12.79         2.70        17.85 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A92D 
       64.57        14.33        73.41        20.81        55.56        66.81 
TCGA-VQ-A94O TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       21.04        38.93        32.94        26.04         0.79 

$`14Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK 
       20.15         9.86        58.03        26.70        11.70         9.47 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       17.29        13.68        39.12        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        40.21        30.90        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 
        9.21        36.16        35.84        18.15        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        9.07        29.56        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
        9.60        32.25         8.05         0.56        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 
        3.32        11.80        31.27        25.05         3.72        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        7.53        26.73        31.96        32.58         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       28.34        13.51        20.42        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8525 
       13.41        13.02        13.15        13.35        12.10        12.59 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        12.30        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        12.00         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
        7.99        25.71        12.66        20.91        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.85        13.35        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        26.43        11.24        11.44        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34         7.13         0.62        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         3.48        19.53        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       13.58         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       30.51         1.51         5.92        24.39        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20        22.75        25.81        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 
       23.80        21.17        14.07        15.68         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39        18.38        12.46        19.53        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       10.62        15.75        13.51         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
      122.30        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31        22.19         2.50         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       15.65        13.35        29.59        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        18.74        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50         9.73         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58         5.72         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       43.66        28.41        17.13        54.12        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.46               0.00 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            115.69             122.30 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            15.390             14.615 
[1] "0.5 - 115.7 (15.4)" "0.0 - 122.3 (14.6)"
[1] "hr=" "1"  
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         0        2        8       11        13        14
  14Q LOSS WILD-TYPE       2       14       33       21        27        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           0         25         18          9        5
  14Q LOSS WILD-TYPE         3         56         45         30       39
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 14
  STAGE IB                  8                 33
  STAGE II                 11                 21
  STAGE IIA                13                 27
  STAGE IIB                14                 42
  STAGE III                 0                  3
  STAGE IIIA               25                 56
  STAGE IIIB               18                 45
  STAGE IIIC                9                 30
  STAGE IV                  5                 39
[1] 11  2
[1] 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     3  21  56  27
  14Q LOSS WILD-TYPE  20  72 140  92
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                3                 20
  T2               21                 72
  T3               56                140
  T4               27                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  14Q LOSS MUTATED   31 27 27 19
  14Q LOSS WILD-TYPE 99 92 59 69
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               31                 99
  N1               27                 92
  N2               27                 59
  N3               19                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    99   3
  14Q LOSS WILD-TYPE 290  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     99    3
  14Q LOSS WILD-TYPE  290   27
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               99                290
  1                3                 27
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    38  73
  14Q LOSS WILD-TYPE 120 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     38   73
  14Q LOSS WILD-TYPE  120  210
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               38                120
  MALE                 73                210
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    83  20
  14Q LOSS WILD-TYPE 239  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     83   20
  14Q LOSS WILD-TYPE  239   56
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                83                239
  YES               20                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  14Q LOSS MUTATED                                          5
  14Q LOSS WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  14Q LOSS MUTATED                                      14
  14Q LOSS WILD-TYPE                                    58
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                       40
  14Q LOSS WILD-TYPE                                                    123
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  14Q LOSS MUTATED                                                   2
  14Q LOSS WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                                  25
  14Q LOSS WILD-TYPE                                                                57
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  14Q LOSS MUTATED                                                    2
  14Q LOSS WILD-TYPE                                                  6
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  14Q LOSS MUTATED                                                 23
  14Q LOSS WILD-TYPE                                               56
D67V9, multiclass
                                                                   clus
vv                                                                  14Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           14
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          40
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               25
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                23
                                                                   clus
vv                                                                  14Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             58
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           123
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 57
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    90   3   2   7
  14Q LOSS WILD-TYPE 259  15  17  18
D67V10, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               90                259
  R1                3                 15
  R2                2                 17
  RX                7                 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"
D67V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  14Q LOSS MUTATED      24                         3
  14Q LOSS WILD-TYPE    64                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           0    75
  14Q LOSS WILD-TYPE                                         1   203
D67V12, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                                   24                 64
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   75                203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     0  83
  14Q LOSS WILD-TYPE   5 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   83
  14Q LOSS WILD-TYPE    5  233
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               83                233
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    52  32
  15Q LOSS WILD-TYPE 194 137
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                84                331 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                32                137 
$`15Q LOSS MUTATED`
TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4257 
        0.23         9.86        27.35        58.03        11.01         9.67 
TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 
       35.24        28.73         3.45        29.42         2.66        14.79 
TCGA-BR-8483 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI 
        5.39        20.88        10.68         0.72        20.65        21.44 
TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48A 
       13.18        12.53         7.17        12.39        12.82        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4466 
       11.61        12.20        20.02         7.99         4.01        18.97 
TCGA-CG-5719 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 
        1.02        12.03        12.66        19.13        20.55        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX 
       10.26        15.22        12.79        14.66        16.44        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-FP-7998 TCGA-FP-A4BF 
       22.29        15.65        19.96         7.99        22.29         5.52 
TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GP 
       26.47        18.15        28.96        22.82        22.75         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD 
        6.58         2.10        12.95        23.84        21.17        33.40 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IP-7968 TCGA-R5-A7ZF 
       12.46        13.35         6.44        11.70         2.53         8.52 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB 
       11.05        16.67        37.91       115.69        35.61         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91U TCGA-VQ-A91X 
       48.79         5.46        13.35        73.41         1.71         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F 
        9.73         9.04        42.54        43.66        32.94        54.12 

$`15Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       26.93        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       39.78        18.15        15.32         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       32.25         8.05         0.56        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       11.80        31.27         7.36        25.05         3.72        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       32.58         9.86         8.22        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.42         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.76        12.59        12.33        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.43         6.31        12.30        11.31 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58        11.77        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        1.02         8.05        54.08        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       12.03         0.00         9.01         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        7.99        25.71        20.91        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        13.35        15.98        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.24        11.44        20.32         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 
       30.51         1.51         5.92        24.39        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 
        6.51        20.25         0.26        29.00        23.80        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
       19.53         6.74        12.59         6.51        10.62        15.75 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        4.60         9.24         8.61         5.13       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z 
       18.74        20.81        32.88        42.64        60.85        55.56 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       21.04         2.66        11.24        18.41        28.41        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.23               0.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            115.69             122.30 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            13.065             15.650 
[1] "0.2 - 115.7 (13.1)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1"  
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         0        1        9        7         8         9
  15Q LOSS WILD-TYPE       2       15       32       25        32        47
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           0         24         14          7        6
  15Q LOSS WILD-TYPE         3         57         49         32       38
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 15
  STAGE IB                  9                 32
  STAGE II                  7                 25
  STAGE IIA                 8                 32
  STAGE IIB                 9                 47
  STAGE III                 0                  3
  STAGE IIIA               24                 57
  STAGE IIIB               14                 49
  STAGE IIIC                7                 32
  STAGE IV                  6                 38
[1] 11  2
[1] 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     2  19  50  17
  15Q LOSS WILD-TYPE  21  74 146 102
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                2                 21
  T2               19                 74
  T3               50                146
  T4               17                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q LOSS MUTATED    23  25  19  19
  15Q LOSS WILD-TYPE 107  94  67  69
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               23                107
  N1               25                 94
  N2               19                 67
  N3               19                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    78   5
  15Q LOSS WILD-TYPE 311  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     78    5
  15Q LOSS WILD-TYPE  311   25
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               78                311
  1                5                 25
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    34  56
  15Q LOSS WILD-TYPE 124 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     34   56
  15Q LOSS WILD-TYPE  124  227
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               34                124
  MALE                 56                227
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    59  22
  15Q LOSS WILD-TYPE 263  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     59   22
  15Q LOSS WILD-TYPE  263   54
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                59                263
  YES               22                 54
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  15Q LOSS MUTATED                                          4
  15Q LOSS WILD-TYPE                                        9
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  15Q LOSS MUTATED                                      12
  15Q LOSS WILD-TYPE                                    60
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                       26
  15Q LOSS WILD-TYPE                                                    137
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  15Q LOSS MUTATED                                                   1
  15Q LOSS WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                                  21
  15Q LOSS WILD-TYPE                                                                61
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  15Q LOSS MUTATED                                                    2
  15Q LOSS WILD-TYPE                                                  6
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  15Q LOSS MUTATED                                                 24
  15Q LOSS WILD-TYPE                                               55
D68V9, multiclass
                                                                   clus
vv                                                                  15Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          26
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               21
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                24
                                                                   clus
vv                                                                  15Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           137
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 61
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  55
[1] 7 2
[1] TRUE
[1] "dimension of 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    73   4   3   3
  15Q LOSS WILD-TYPE 276  14  16  22
D68V10, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               73                276
  R1                4                 14
  R2                3                 16
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  15Q LOSS MUTATED      23                         1
  15Q LOSS WILD-TYPE    65                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           0    56
  15Q LOSS WILD-TYPE                                         1   222
D68V12, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                                   23                 65
  BLACK OR AFRICAN AMERICAN                                1                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   56                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2  67
  15Q LOSS WILD-TYPE   3 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   67
  15Q LOSS WILD-TYPE    3  249
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               67                249
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    59  35
  16P LOSS WILD-TYPE 187 134
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                94                321 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                35                134 
$`16P LOSS MUTATED`
TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-7197 
       16.24        27.35        26.93         6.61         4.08         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 
       35.24        33.63        39.78         3.45        33.21        11.44 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 
        0.69        29.42         2.66        19.96        17.52        14.79 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       26.73        24.79         8.22        34.98         1.48         0.72 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        1.15        21.44        11.21        12.76        12.59        12.53 
TCGA-CD-8530 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4436 
       12.39         6.31        12.43        11.61        12.20         7.99 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6519 
       29.98        19.07        12.03        12.03        20.91        20.55 
TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
       15.22        12.33        11.31        22.29        15.65        19.96 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 
        7.99        72.23        63.06         5.92        18.15        22.82 
TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H4 
        0.76        22.75        25.81        11.77         6.58        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RN TCGA-IN-A6RR TCGA-KB-A6F5 
       23.80        21.17        33.40        19.53         6.74         5.56 
TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N9 
       37.64        14.04         6.08        11.05        16.67        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PE 
        5.79        48.79         5.46        18.48        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91A 
       12.79         2.70        17.85         1.87        64.57        39.45 
TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-AA68 
       18.74         9.50        55.56         9.04        66.81        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       38.93        17.13        27.55         0.79 

$`16P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        9.86        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
       31.20        44.94        21.90        36.16        35.84        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       15.32        28.73         9.07        29.56        37.25        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 
       29.59         9.60        32.25         8.05         0.56         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 
        9.34        28.14         6.28         7.53        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        20.88        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65        20.42        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8527 TCGA-CD-8528 
       13.15        13.18        13.35        12.10         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        12.30        11.31         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       54.08         4.01        14.01         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
       20.32         8.38         4.34         7.13         0.62        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       24.39        28.96        22.32        21.07        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.26        22.68        24.20         3.25        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.95        29.00        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        13.35         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 
        2.53        63.62        36.95         3.72        19.73        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT 
       18.21         8.52        74.53         4.60         9.24         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87        19.04         0.92 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF 
       37.22         7.73        30.97        34.29        16.31         2.50 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY 
        9.27        23.41        15.65        13.35        29.59        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       73.41        11.70        21.83        61.22        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 
        1.71        42.64        60.85         9.73         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58         5.72        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       11.24        18.41        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        12.43        17.26 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.69               0.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             72.23             122.30 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            16.455             14.430 
[1] "0.7 - 72.2 (16.5)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         0        5        9        9        11        11
  16P LOSS WILD-TYPE       2       11       32       23        29        45
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           1         24         11          8        7
  16P LOSS WILD-TYPE         2         57         52         31       37
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  5                 11
  STAGE IB                  9                 32
  STAGE II                  9                 23
  STAGE IIA                11                 29
  STAGE IIB                11                 45
  STAGE III                 1                  2
  STAGE IIIA               24                 57
  STAGE IIIB               11                 52
  STAGE IIIC                8                 31
  STAGE IV                  7                 37
[1] 11  2
[1] 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     5  19  50  24
  16P LOSS WILD-TYPE  18  74 146  95
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                5                 18
  T2               19                 74
  T3               50                146
  T4               24                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P LOSS MUTATED    30  31  17  18
  16P LOSS WILD-TYPE 100  88  69  70
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               30                100
  N1               31                 88
  N2               17                 69
  N3               18                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    93   3
  16P LOSS WILD-TYPE 296  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     93    3
  16P LOSS WILD-TYPE  296   27
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               93                296
  1                3                 27
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    38  62
  16P LOSS WILD-TYPE 120 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     38   62
  16P LOSS WILD-TYPE  120  221
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               38                120
  MALE                 62                221
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    73  20
  16P LOSS WILD-TYPE 249  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     73   20
  16P LOSS WILD-TYPE  249   56
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                73                249
  YES               20                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  16P LOSS MUTATED                                          3
  16P LOSS WILD-TYPE                                       10
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  16P LOSS MUTATED                                       9
  16P LOSS WILD-TYPE                                    63
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                       30
  16P LOSS WILD-TYPE                                                    133
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  16P LOSS MUTATED                                                   8
  16P LOSS WILD-TYPE                                                13
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                                  18
  16P LOSS WILD-TYPE                                                                64
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  16P LOSS MUTATED                                                    2
  16P LOSS WILD-TYPE                                                  6
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  16P LOSS MUTATED                                                 29
  16P LOSS WILD-TYPE                                               50
D69V9, multiclass
                                                                   clus
vv                                                                  16P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          30
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                29
                                                                   clus
vv                                                                  16P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           133
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  50
[1] 7 2
[1] TRUE
[1] "dimension of 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    80   5   2   5
  16P LOSS WILD-TYPE 269  13  17  20
D69V10, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               80                269
  R1                5                 13
  R2                2                 17
  RX                5                 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"
D69V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16P LOSS MUTATED      24                         4
  16P LOSS WILD-TYPE    64                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           0    57
  16P LOSS WILD-TYPE                                         1   221
D69V12, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                                   24                 64
  BLACK OR AFRICAN AMERICAN                                4                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   57                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0  68
  16P LOSS WILD-TYPE   5 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0   68
  16P LOSS WILD-TYPE    5  248
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               68                248
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    69  40
  16Q LOSS WILD-TYPE 177 129
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               109                306 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                40                129 
$`16Q LOSS MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U 
       47.05        22.98        16.24        20.15        27.35        26.93 
TCGA-3M-AB46 TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6564 
       58.03         9.44         6.61         4.08        17.29        26.10 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 
        9.21        35.24        33.63        39.78        28.73         3.45 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 
       33.21        11.44         0.69         9.60        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 
       19.96        17.52        14.79        25.18        26.73        24.79 
TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 
        8.22         0.72        20.65         1.15        21.44        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 
       13.35        11.21        12.76        12.59        12.53        12.39 
TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4443 
       12.07         6.31        12.43        12.20         7.99        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4477 TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6519 
       19.07        12.03        30.97        12.03        20.91        20.55 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A6EX 
       17.19        15.22        12.79        18.21        14.27        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-F1-6875 TCGA-HF-7133 TCGA-HU-8243 
       22.29        15.65         8.38        72.23        63.06         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4GY 
       18.15        22.82         0.76        11.77         6.58         0.26 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN 
       23.84        23.80        21.17        33.40        18.38        19.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A8N9 
        5.56        63.62        37.64         6.08        11.05        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
        5.79        48.79         5.46        18.48         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX 
       22.19        12.79         2.70        17.85         1.87        64.57 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       39.45        18.74        32.88         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D 
        9.04         4.54        66.81        43.66        38.93        17.13 
TCGA-ZQ-A9CR 
        0.79 

$`16Q LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 
       21.99        79.07         0.23         9.86        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       19.56        11.01         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       44.94        21.90        36.16        35.84        18.15        15.32 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 
        9.07        29.56        37.25        14.43        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        8.05         0.56         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       31.10        13.08         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       25.05         3.72         5.39         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL 
        0.66        32.52        13.51         0.46        20.42        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8527 
        5.13        13.41        13.02        13.18        12.10         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
       12.33        12.30        12.59        11.64        15.39        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       12.43        12.30        11.31        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4462 TCGA-CG-4465 
        8.05        54.08         4.01        14.01         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        12.00         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       13.35        10.26        15.98        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       26.43        11.24        11.44        20.32         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51        26.47         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.32        21.07        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.51        20.25         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       29.00        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39        12.46        13.35         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW 
        8.52        74.53         4.60         9.24         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87        19.04         0.92 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO 
       37.22        30.97        34.29        16.31         2.50         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        13.35        29.59        14.33        73.41 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       11.70        21.83        61.22        20.81         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
       60.85         2.01        55.43         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        2.66        42.54        11.24        18.41        28.41        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.26               0.00 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             72.23             122.30 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             17.19              14.25 
[1] "0.3 - 72.2 (17.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         1        5       11       12        10        13
  16Q LOSS WILD-TYPE       1       11       30       20        30        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           1         30         12          9        7
  16Q LOSS WILD-TYPE         2         51         51         30       37
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  5                 11
  STAGE IB                 11                 30
  STAGE II                 12                 20
  STAGE IIA                10                 30
  STAGE IIB                13                 43
  STAGE III                 1                  2
  STAGE IIIA               30                 51
  STAGE IIIB               12                 51
  STAGE IIIC                9                 30
  STAGE IV                  7                 37
[1] 11  2
[1] 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     7  22  56  28
  16Q LOSS WILD-TYPE  16  71 140  91
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                7                 16
  T2               22                 71
  T3               56                140
  T4               28                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16Q LOSS MUTATED   36 32 20 22
  16Q LOSS WILD-TYPE 94 87 66 66
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               36                 94
  N1               32                 87
  N2               20                 66
  N3               22                 66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   108   3
  16Q LOSS WILD-TYPE 281  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    108    3
  16Q LOSS WILD-TYPE  281   27
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              108                281
  1                3                 27
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    44  70
  16Q LOSS WILD-TYPE 114 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     44   70
  16Q LOSS WILD-TYPE  114  213
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               44                114
  MALE                 70                213
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    81  27
  16Q LOSS WILD-TYPE 241  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     81   27
  16Q LOSS WILD-TYPE  241   49
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                81                241
  YES               27                 49
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  16Q LOSS MUTATED                                          4
  16Q LOSS WILD-TYPE                                        9
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  16Q LOSS MUTATED                                      13
  16Q LOSS WILD-TYPE                                    59
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                       32
  16Q LOSS WILD-TYPE                                                    131
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  16Q LOSS MUTATED                                                   9
  16Q LOSS WILD-TYPE                                                12
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                                  19
  16Q LOSS WILD-TYPE                                                                63
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  16Q LOSS MUTATED                                                    3
  16Q LOSS WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  16Q LOSS MUTATED                                                 32
  16Q LOSS WILD-TYPE                                               47
D70V9, multiclass
                                                                   clus
vv                                                                  16Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           13
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          32
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               19
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                32
                                                                   clus
vv                                                                  16Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             59
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 12
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  47
[1] 7 2
[1] TRUE
[1] "dimension of 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    93   5   4   4
  16Q LOSS WILD-TYPE 256  13  15  21
D70V10, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               93                256
  R1                5                 13
  R2                4                 15
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16Q LOSS MUTATED      25                         4
  16Q LOSS WILD-TYPE    63                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           0    66
  16Q LOSS WILD-TYPE                                         1   212
D70V12, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                                   25                 63
  BLACK OR AFRICAN AMERICAN                                4                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   66                212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  73
  16Q LOSS WILD-TYPE   4 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   73
  16Q LOSS WILD-TYPE    4  243
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               73                243
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    95  64
  17P LOSS WILD-TYPE 151 105
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               159                256 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                64                105 
$`17P LOSS MUTATED`
TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       47.05        79.07         0.23         9.86        27.35        26.93 
TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 
       58.03        11.70        11.01         9.44         6.61         9.67 
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 
        6.18        17.29        19.33         9.17        12.16         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 
       35.24        33.63        28.73        33.21        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8362 
        9.60        29.42         2.66        19.96        15.58        13.08 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8678 TCGA-BR-8682 
       14.04        14.79         5.39        25.18        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.86        10.68        13.87         7.53        34.98         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 
        0.72        13.51        20.65        20.42         1.15        13.02 
TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       13.15        12.76        12.59         7.17        12.33        12.30 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       15.39        12.82         6.31        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 
       12.20        20.02         3.02        27.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 
       54.08         4.01        29.98        19.07         7.07        30.97 
TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6519 
        1.02        15.02         4.01        69.04        20.91        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.54        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 
       15.98        11.31        14.66        16.44        11.31        15.65 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 
       19.96         7.99        11.38        14.07        17.06        13.58 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 
        6.21        77.29        63.06         1.51        18.15        28.96 
TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 
       22.82        22.75        11.77         8.98         6.58         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       12.95        23.80        36.36        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
       13.35        12.59        11.70        15.75         2.53         5.56 
TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 
       37.64        36.95        45.67         9.24         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
      115.69         8.94         5.79         0.92         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH 
       13.02        18.48        43.36         7.73        46.26        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PY 
        2.70        17.85         1.87        13.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A92D 
       73.41        18.74        20.81        42.64         9.50        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       11.24        18.41        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       27.55        12.43         0.79 

$`17P LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-B7-5816 TCGA-B7-A5TI 
       21.99        22.98        16.24        20.15        26.70        19.56 
TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         4.08         9.34         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       15.95        13.87        13.68        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       31.20        44.94        21.90        36.16        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       18.15        15.32         3.45         9.07        29.56        37.25 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 
       14.43        29.59        32.25         8.05         0.56         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        7.36        25.05         3.72         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 
       26.73        31.96        20.88         8.22        34.13         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL 
       28.34         0.66        32.52         0.46        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
        5.13        13.41        13.18        13.35        11.21        12.10 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 
       12.53        12.39        12.59        11.64        12.07        12.43 
TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 
       12.30         6.58        11.77        12.62        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 
       14.01        12.03         0.00         9.01        18.97        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       12.03        28.96        65.10        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-6818 
       12.66        19.13        18.61        17.85        12.79        12.36 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34         7.13         0.62        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         3.48        19.53        22.29        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
        0.56         5.52        52.21        30.51        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       24.39        22.32        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ 
       24.26        22.68        24.20         3.25        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
       29.98         0.10         6.51        20.25         0.26        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       23.84        21.17        14.07        15.68        33.40         3.45 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT 
       12.46        19.53         6.44         6.74         6.51        10.62 
TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE 
       13.51        63.62         3.72        19.73        14.04        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW 
        8.52        74.53         6.08         4.60        11.05         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       35.61        16.87        19.04        48.79        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       38.14        37.22        30.97        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A 
        2.50         9.27        23.41        15.65        29.59        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       11.70        21.83        61.22        32.88         1.71        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA68 
        6.58         5.72        21.04         2.66        42.54        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-ZA-A8F6 
       28.41        38.93        17.13        17.26 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.23               0.00 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            115.69             122.30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            13.510             16.275 
[1] "0.2 - 115.7 (13.5)" "0.0 - 122.3 (16.3)"
[1] "hr=" "1"  
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         1        6       16       15        14        22
  17P LOSS WILD-TYPE       1       10       25       17        26        34
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           0         30         27          9       17
  17P LOSS WILD-TYPE         3         51         36         30       27
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  6                 10
  STAGE IB                 16                 25
  STAGE II                 15                 17
  STAGE IIA                14                 26
  STAGE IIB                22                 34
  STAGE III                 0                  3
  STAGE IIIA               30                 51
  STAGE IIIB               27                 36
  STAGE IIIC                9                 30
  STAGE IV                 17                 27
[1] 11  2
[1] 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     8  40  78  36
  17P LOSS WILD-TYPE  15  53 118  83
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                8                 15
  T2               40                 53
  T3               78                118
  T4               36                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  17P LOSS MUTATED   51 42 36 31
  17P LOSS WILD-TYPE 79 77 50 57
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               51                 79
  N1               42                 77
  N2               36                 50
  N3               31                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   146   9
  17P LOSS WILD-TYPE 243  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    146    9
  17P LOSS WILD-TYPE  243   21
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              146                243
  1                9                 21
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    49 115
  17P LOSS WILD-TYPE 109 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     49  115
  17P LOSS WILD-TYPE  109  168
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               49                109
  MALE                115                168
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   114  34
  17P LOSS WILD-TYPE 208  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    114   34
  17P LOSS WILD-TYPE  208   42
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               114                208
  YES               34                 42
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  17P LOSS MUTATED                                          7
  17P LOSS WILD-TYPE                                        6
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  17P LOSS MUTATED                                      16
  17P LOSS WILD-TYPE                                    56
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                       54
  17P LOSS WILD-TYPE                                                    109
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  17P LOSS MUTATED                                                  10
  17P LOSS WILD-TYPE                                                11
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                                  40
  17P LOSS WILD-TYPE                                                                42
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  17P LOSS MUTATED                                                    4
  17P LOSS WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  17P LOSS MUTATED                                                 33
  17P LOSS WILD-TYPE                                               46
D71V9, multiclass
                                                                   clus
vv                                                                  17P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          54
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                33
                                                                   clus
vv                                                                  17P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             56
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           109
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 42
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  46
[1] 7 2
[1] TRUE
[1] "dimension of 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   131   9   6   5
  17P LOSS WILD-TYPE 218   9  13  20
D71V10, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              131                218
  R1                9                  9
  R2                6                 13
  RX                5                 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"
D71V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17P LOSS MUTATED      34                         3
  17P LOSS WILD-TYPE    54                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           1    98
  17P LOSS WILD-TYPE                                         0   180
D71V12, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                                   34                 54
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   98                180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     2 107
  17P LOSS WILD-TYPE   3 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2  107
  17P LOSS WILD-TYPE    3  209
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              107                209
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    44  27
  17Q LOSS WILD-TYPE 202 142
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                71                344 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                27                142 
$`17Q LOSS MUTATED`
TCGA-CG-4444 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-B7-A5TJ TCGA-BR-4257 
       47.05         0.23         9.86        26.93        11.01         9.67 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8077 
       19.33         9.17        35.24        28.73        33.21         0.69 
TCGA-BR-8291 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 
       19.96        14.79         9.21         9.86        10.68         7.53 
TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 
       34.98         0.72        13.51        20.65         1.15        13.02 
TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48C 
       12.76        12.33        15.39        12.82        11.31        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 
       12.20        20.02         3.02        54.08         4.01        19.07 
TCGA-CG-4477 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       30.97        20.91        20.55        17.19        10.26        15.22 
TCGA-D7-6820 TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-HU-8245 TCGA-HU-8249 
       11.31        11.31        15.65         7.99        18.15        28.96 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-IN-8663 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7O7 
       22.75         8.98         3.39         5.56        37.64        45.67 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU 
        8.61        16.67       115.69         8.94         5.79         5.46 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PX TCGA-VQ-A91N TCGA-VQ-A91X 
       46.26        12.79        17.85        64.57        18.74         9.50 
TCGA-VQ-A91Y TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        9.73        32.94        54.12        27.55         0.79 

$`17Q LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU 
       21.99        22.98        79.07        16.24        20.15        27.35 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       15.32         3.45         9.07        29.56        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        7.36        25.05         3.72         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53        26.73        24.79        31.96        32.58        20.88 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
        8.22        34.13        13.87         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        32.52         0.46        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
       12.10        12.59        12.53         7.17        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       12.59        11.64        12.07        12.43         6.31        12.30 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 
       12.43         6.58        11.77        12.62        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
        1.02         7.99         8.05        14.01        29.98        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        25.71        12.66        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 
       18.54        18.61        17.85        13.35        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        22.29         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        24.26        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        14.04        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60         9.24        11.05         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       19.04         0.92        48.79        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       30.97        34.29        16.31        22.19         2.50         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z 
       20.81        32.88         1.71        42.64        60.85        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        28.41        38.93        17.13        26.04        16.14 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.23               0.00 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            115.69             122.30 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             13.02              15.45 
[1] "0.2 - 115.7 (13.0)" "0.0 - 122.3 (15.4)"
[1] "hr=" "1"  
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         0        1        5        6         5        13
  17Q LOSS WILD-TYPE       2       15       36       26        35        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           0         17         13          4        6
  17Q LOSS WILD-TYPE         3         64         50         35       38
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 15
  STAGE IB                  5                 36
  STAGE II                  6                 26
  STAGE IIA                 5                 35
  STAGE IIB                13                 43
  STAGE III                 0                  3
  STAGE IIIA               17                 64
  STAGE IIIB               13                 50
  STAGE IIIC                4                 35
  STAGE IV                  6                 38
[1] 11  2
[1] 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     1  15  35  21
  17Q LOSS WILD-TYPE  22  78 161  98
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                1                 22
  T2               15                 78
  T3               35                161
  T4               21                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q LOSS MUTATED    17  24  18  12
  17Q LOSS WILD-TYPE 113  95  68  76
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               17                113
  N1               24                 95
  N2               18                 68
  N3               12                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    67   3
  17Q LOSS WILD-TYPE 322  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     67    3
  17Q LOSS WILD-TYPE  322   27
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               67                322
  1                3                 27
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    27  47
  17Q LOSS WILD-TYPE 131 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     27   47
  17Q LOSS WILD-TYPE  131  236
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               27                131
  MALE                 47                236
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    52  13
  17Q LOSS WILD-TYPE 270  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     52   13
  17Q LOSS WILD-TYPE  270   63
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                52                270
  YES               13                 63
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  17Q LOSS MUTATED                                          3
  17Q LOSS WILD-TYPE                                       10
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  17Q LOSS MUTATED                                       7
  17Q LOSS WILD-TYPE                                    65
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                       22
  17Q LOSS WILD-TYPE                                                    141
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  17Q LOSS MUTATED                                                   4
  17Q LOSS WILD-TYPE                                                17
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                                  19
  17Q LOSS WILD-TYPE                                                                63
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  17Q LOSS MUTATED                                                    2
  17Q LOSS WILD-TYPE                                                  6
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  17Q LOSS MUTATED                                                 17
  17Q LOSS WILD-TYPE                                               62
D72V9, multiclass
                                                                   clus
vv                                                                  17Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               19
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                17
                                                                   clus
vv                                                                  17Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  62
[1] 7 2
[1] TRUE
[1] "dimension of 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    57   3   4   3
  17Q LOSS WILD-TYPE 292  15  15  22
D72V10, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               57                292
  R1                3                 15
  R2                4                 15
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17Q LOSS MUTATED      16                         1
  17Q LOSS WILD-TYPE    72                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           1    45
  17Q LOSS WILD-TYPE                                         0   233
D72V12, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                                   16                 72
  BLACK OR AFRICAN AMERICAN                                1                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   45                233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  51
  17Q LOSS WILD-TYPE   4 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   51
  17Q LOSS WILD-TYPE    4  265
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               51                265
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    74  41
  18P LOSS WILD-TYPE 172 128
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               115                300 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                41                128 
$`18P LOSS MUTATED`
TCGA-CG-4444 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TI 
       47.05         0.23        20.15        26.93        58.03        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4255 TCGA-BR-4279 TCGA-BR-6456 
       11.01         9.47         9.44         4.08         9.57        17.29 
TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       13.68        26.10        12.16        35.24        33.63        39.78 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8366 
       28.73         9.07         2.66        19.96        22.19         0.95 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8683 
       14.04         3.32        25.18        27.12        24.79         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       20.88        10.68         7.53        34.98         1.48        12.89 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
       13.18        11.21        12.76        12.59         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A489 TCGA-CD-A48A 
       12.30        11.64        15.39        12.07        11.31        12.43 
TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 
       11.61         7.99         8.05        54.08         4.01        19.07 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5732 TCGA-D7-6518 TCGA-D7-6519 
        7.07        30.97         1.02        69.04        19.13        20.55 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 
       18.54        13.35        15.98        19.50        18.21        21.14 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-EQ-5647 TCGA-F1-6875 
       16.44        36.43        11.24        20.32         0.62        72.23 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-HU-8238 
       11.38        19.53        14.07        22.29        17.06         1.51 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G6 TCGA-HU-A4GH 
       18.15        28.96        22.82        21.07        24.26        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-A6RL 
        8.98         6.58         2.10        12.95        21.17        13.35 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7O7 
       11.70        13.51         5.56        37.64        36.95        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-SW-A7EB TCGA-VQ-A8DT 
       18.21         8.52        16.67       115.69         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PD TCGA-VQ-A8PF 
        5.46        13.02        18.48        43.36        16.31         2.50 
TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA6B 
       42.64        55.56         4.54        66.81        42.54        32.94 
TCGA-VQ-AA6K 
       12.43 

$`18P LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU 
       21.99        22.98        79.07        16.24         9.86        27.35 
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        19.33        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7958 
       36.16        35.84        18.15        15.32         3.45        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 
        9.60        32.25         8.05         0.56        29.42         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       17.52        26.33         4.31        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       26.73        31.96        32.58         8.22        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        6.08        27.55        28.57         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8526 
       13.41        13.02        13.15        13.35        12.10        12.53 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       12.39        12.59        12.82        12.43         6.31        12.30 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
       27.02        15.95         1.02        14.01        29.98        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97        12.00         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       12.66        20.91        18.84        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       24.72        16.80        17.19        14.66        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
        5.92        13.78        14.76        26.43        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 
        7.99        14.47        21.27         3.48        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       52.21        30.51        26.47         5.92        24.39        22.32 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
       20.25         0.26        29.00        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG 
        6.51        10.62        15.75         2.53        63.62         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       19.73        14.04        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       19.04         0.92        13.25        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PE 
       37.22         7.73        30.97        34.29        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       39.45        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 
       32.88         1.71        60.85         9.50         9.73         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        21.04         2.66 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       11.24        18.41        43.66        28.41        38.93        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        27.55        17.26         0.79 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.23               0.00 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            115.69             122.30 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            15.390             14.775 
[1] "0.2 - 115.7 (15.4)" "0.0 - 122.3 (14.8)"
[1] "hr=" "1.2"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         0        4        8       11        13        14
  18P LOSS WILD-TYPE       2       12       33       21        27        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED           0         25         17          9       12
  18P LOSS WILD-TYPE         3         56         46         30       32
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  4                 12
  STAGE IB                  8                 33
  STAGE II                 11                 21
  STAGE IIA                13                 27
  STAGE IIB                14                 42
  STAGE III                 0                  3
  STAGE IIIA               25                 56
  STAGE IIIB               17                 46
  STAGE IIIC                9                 30
  STAGE IV                 12                 32
[1] 11  2
[1] 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     3  25  60  30
  18P LOSS WILD-TYPE  20  68 136  89
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                3                 20
  T2               25                 68
  T3               60                136
  T4               30                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18P LOSS MUTATED   35 27 26 26
  18P LOSS WILD-TYPE 95 92 60 62
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               35                 95
  N1               27                 92
  N2               26                 60
  N3               26                 62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   105   9
  18P LOSS WILD-TYPE 284  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    105    9
  18P LOSS WILD-TYPE  284   21
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              105                284
  1                9                 21
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    33  86
  18P LOSS WILD-TYPE 125 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     33   86
  18P LOSS WILD-TYPE  125  197
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               33                125
  MALE                 86                197
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    90  21
  18P LOSS WILD-TYPE 232  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     90   21
  18P LOSS WILD-TYPE  232   55
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                90                232
  YES               21                 55
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  18P LOSS MUTATED                                          5
  18P LOSS WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  18P LOSS MUTATED                                      21
  18P LOSS WILD-TYPE                                    51
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                       39
  18P LOSS WILD-TYPE                                                    124
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  18P LOSS MUTATED                                                   5
  18P LOSS WILD-TYPE                                                16
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                                  22
  18P LOSS WILD-TYPE                                                                60
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  18P LOSS MUTATED                                                    2
  18P LOSS WILD-TYPE                                                  6
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  18P LOSS MUTATED                                                 25
  18P LOSS WILD-TYPE                                               54
D73V9, multiclass
                                                                   clus
vv                                                                  18P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           21
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          39
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               22
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                25
                                                                   clus
vv                                                                  18P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             51
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           124
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  54
[1] 7 2
[1] TRUE
[1] "dimension of 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    93   5   4   4
  18P LOSS WILD-TYPE 256  13  15  21
D73V10, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               93                256
  R1                5                 13
  R2                4                 15
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED      34                         4
  18P LOSS WILD-TYPE    54                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           0    67
  18P LOSS WILD-TYPE                                         1   211
D73V12, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                                   34                 54
  BLACK OR AFRICAN AMERICAN                                4                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   67                211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  87
  18P LOSS WILD-TYPE   2 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   87
  18P LOSS WILD-TYPE    2  229
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               87                229
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    89  58
  18Q LOSS WILD-TYPE 157 111
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               147                268 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                58                111 
$`18Q LOSS MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U 
       47.05        22.98         0.23        20.15        27.35        26.93 
TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       58.03        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 
        6.61         4.08         6.18         9.57        17.29        13.68 
TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
       26.10        12.16        35.24        33.63        39.78        28.73 
TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 
        9.07        11.44        19.96        22.19         0.95        14.04 
TCGA-BR-8370 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 
        3.32        20.22        27.12        26.73        24.79         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       20.88         8.22        10.68        13.87         7.53        34.98 
TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
       12.89         0.66        13.18        13.35        11.21        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 
       12.59        12.53         7.17        12.33        12.30        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
       15.39        12.07         6.31        12.43        11.61        12.20 
TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 
        3.02         7.99         8.05        54.08         4.01        19.07 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 
       18.97         7.07        30.97         1.02        12.03         4.01 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 
       69.04        25.71        19.13        20.55        18.54        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 
       17.19        10.26        15.98        19.50        18.21        14.66 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 
       21.14        16.44        36.43        11.24        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C 
       15.65        19.96         0.62         7.99        72.23        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-HU-8249 TCGA-HU-8604 
       19.53        14.07        22.29        17.06        28.96        22.82 
TCGA-HU-8608 TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 
       21.07        24.26        11.77         8.98         6.58         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU 
       12.95        21.17        13.35         6.74        10.62        11.70 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE 
       13.51         5.56        63.62        37.64        45.67        18.21 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.67        37.91       115.69         5.79        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PD 
       13.25        13.02        18.48        43.36         7.73        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91V TCGA-VQ-A91X 
       22.19         2.50        17.85        13.35        42.64         9.50 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T 
       55.56         2.01         4.54        66.81        42.54        11.24 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6K 
       38.93        32.94        12.43 

$`18Q LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-B7-5816 TCGA-BR-4184 
       21.99        79.07        16.24         9.86        26.70         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        4.64         7.43        18.35        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 
        9.67         6.61        34.68        15.95        13.87        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 
        9.21        36.16        35.84        18.15        15.32         3.45 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        14.43         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 
        0.26        17.52        26.33         4.31        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21         1.12        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS 
        7.53        31.96        32.58        34.13         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 
       13.15        12.10        12.39        12.59        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.30        11.31         6.58        11.77        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
       27.02        15.95         1.02        14.01        29.98        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
        0.00         9.01        12.00         6.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 
       21.07         7.99        12.66        20.91        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        15.22        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       24.72        16.80        17.19        20.91        14.27         5.92 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 
       13.78        14.76        26.43        11.31        11.44         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 
        4.34         7.13        14.47        21.27         3.48        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       24.39        18.15        22.32         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
       29.98         0.10         6.51        20.25         0.26        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A93J 
        6.44        12.59         6.51        15.75         2.53        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73        14.04         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
       40.64       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       16.87        19.04         0.92        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       37.22        30.97        34.29        46.26        12.79         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       18.74        20.81        32.88         1.71        60.85         9.73 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
        9.04        55.43         6.58         5.72        21.04         2.66 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        17.26         0.79 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.23               0.00 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            115.69             122.30 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             13.87              15.45 
[1] "0.2 - 115.7 (13.9)" "0.0 - 122.3 (15.4)"
[1] "hr=" "1"  
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         0        5       15       12        15        18
  18Q LOSS WILD-TYPE       2       11       26       20        25        38
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED           0         34         25         10       13
  18Q LOSS WILD-TYPE         3         47         38         29       31
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  5                 11
  STAGE IB                 15                 26
  STAGE II                 12                 20
  STAGE IIA                15                 25
  STAGE IIB                18                 38
  STAGE III                 0                  3
  STAGE IIIA               34                 47
  STAGE IIIB               25                 38
  STAGE IIIC               10                 29
  STAGE IV                 13                 31
[1] 11  2
[1] 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     5  34  83  30
  18Q LOSS WILD-TYPE  18  59 113  89
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                5                 18
  T2               34                 59
  T3               83                113
  T4               30                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18Q LOSS MUTATED   45 39 32 32
  18Q LOSS WILD-TYPE 85 80 54 56
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               45                 85
  N1               39                 80
  N2               32                 54
  N3               32                 56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   137  10
  18Q LOSS WILD-TYPE 252  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    137   10
  18Q LOSS WILD-TYPE  252   20
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              137                252
  1               10                 20
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    52 102
  18Q LOSS WILD-TYPE 106 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     52  102
  18Q LOSS WILD-TYPE  106  181
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               52                106
  MALE                102                181
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   112  30
  18Q LOSS WILD-TYPE 210  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    112   30
  18Q LOSS WILD-TYPE  210   46
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               112                210
  YES               30                 46
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  18Q LOSS MUTATED                                          5
  18Q LOSS WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  18Q LOSS MUTATED                                      22
  18Q LOSS WILD-TYPE                                    50
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                       54
  18Q LOSS WILD-TYPE                                                    109
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  18Q LOSS MUTATED                                                   5
  18Q LOSS WILD-TYPE                                                16
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                                  34
  18Q LOSS WILD-TYPE                                                                48
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  18Q LOSS MUTATED                                                    2
  18Q LOSS WILD-TYPE                                                  6
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  18Q LOSS MUTATED                                                 31
  18Q LOSS WILD-TYPE                                               48
D74V9, multiclass
                                                                   clus
vv                                                                  18Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           22
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          54
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               34
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                31
                                                                   clus
vv                                                                  18Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             50
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           109
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 48
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  48
[1] 7 2
[1] TRUE
[1] "dimension of 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   117   7   7   8
  18Q LOSS WILD-TYPE 232  11  12  17
D74V10, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              117                232
  R1                7                 11
  R2                7                 12
  RX                8                 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"
D74V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18Q LOSS MUTATED      35                         3
  18Q LOSS WILD-TYPE    53                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           0    94
  18Q LOSS WILD-TYPE                                         1   184
D74V12, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                                   35                 53
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   94                184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V13, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3 106
  18Q LOSS WILD-TYPE   2 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3  106
  18Q LOSS WILD-TYPE    2  210
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO              106                210
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    61  49
  19P LOSS WILD-TYPE 185 120
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               110                305 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                49                120 
$`19P LOSS MUTATED`
TCGA-VQ-A8PU TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 
       27.35        19.56        11.01         9.44         6.61         9.67 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
       19.33         9.17        35.24        33.63        39.78        28.73 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 
        3.45        11.44         0.69         2.66         2.20        14.04 
TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4CS 
       14.79         9.21        24.79        10.68        34.98         1.48 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 
        0.72        20.65         1.15        13.02        13.15        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
       12.76        12.59         7.17         6.31        11.31        12.43 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       12.20        20.02         7.99        54.08         4.01        29.98 
TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6520 TCGA-D7-6525 
       18.97        12.03        15.02        69.04        18.84        13.35 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A6EX TCGA-D7-A6F0 
       10.26        12.79        11.31        19.50        11.31        22.29 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7916 TCGA-FP-8099 
       15.65         0.62         7.99        72.23        14.07        17.06 
TCGA-FP-8631 TCGA-FP-A9TM TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP 
        0.56         6.21         5.92        18.15        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        6.58         2.10        23.84        23.80        21.17        33.40 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 
        3.39        18.38        12.59        10.62        11.70         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT 
       63.62        37.64        45.67        18.21         6.08         8.61 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        5.13        37.91         8.94         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PK 
       13.25        13.02        18.48        43.36         7.73        17.85 
TCGA-VQ-A8PM TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
        1.87        18.74         1.71        42.64         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       55.56         9.04         2.01        43.66        38.93        17.13 
TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       27.55         0.79 

$`19P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       20.15         9.86        26.93        58.03        26.70        11.70 
TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 
        9.21        36.16        35.84        18.15        15.32         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
       29.56        33.21        37.25        14.43        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 
       32.25         8.05         0.56        29.42        19.96        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88         8.22        34.13        13.87         7.53         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51         0.46        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
       21.44        16.14         5.13        13.41        13.18        13.35 
TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       11.21        12.53        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       11.64        15.39        12.07        12.82        12.43        12.30 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       11.61         6.58        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 
       15.95         1.02         8.05        14.01        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
       12.66        20.91        19.13        20.55        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 
       17.85        17.19        15.22        15.98        12.36        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 
       14.76        26.43        11.24        11.44        20.32         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        4.34        19.96         7.13        14.47        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        19.53        22.29        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        22.75        25.81        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 
        6.51        20.25         0.26        12.95        29.00        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL 
       15.68        36.36         3.45        18.81        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
       19.53         6.44         6.74         6.51        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF 
        2.53        36.95         3.72        19.73        14.04         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV 
       74.53         4.60         9.24        11.05        16.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       16.87        19.04         5.79        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
       37.22        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        12.79         2.70         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W 
       11.70        21.83        61.22        20.81        32.88        60.85 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        2.66        42.54        11.24        18.41        28.41        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        12.43        17.26 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.56               0.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             72.23             122.30 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             12.59              16.14 
[1] "0.6 - 72.2 (12.6)"  "0.0 - 122.3 (16.1)"
[1] "hr=" "1.3"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         1        5       10        6        12        16
  19P LOSS WILD-TYPE       1       11       31       26        28        40
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           1         24         13         11       12
  19P LOSS WILD-TYPE         2         57         50         28       32
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  5                 11
  STAGE IB                 10                 31
  STAGE II                  6                 26
  STAGE IIA                12                 28
  STAGE IIB                16                 40
  STAGE III                 1                  2
  STAGE IIIA               24                 57
  STAGE IIIB               13                 50
  STAGE IIIC               11                 28
  STAGE IV                 12                 32
[1] 11  2
[1] 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     7  23  52  31
  19P LOSS WILD-TYPE  16  70 144  88
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                7                 16
  T2               23                 70
  T3               52                144
  T4               31                 88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  19P LOSS MUTATED   32 29 22 27
  19P LOSS WILD-TYPE 98 90 64 61
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               32                 98
  N1               29                 90
  N2               22                 64
  N3               27                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   105   6
  19P LOSS WILD-TYPE 284  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    105    6
  19P LOSS WILD-TYPE  284   24
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0              105                284
  1                6                 24
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    41  75
  19P LOSS WILD-TYPE 117 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     41   75
  19P LOSS WILD-TYPE  117  208
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               41                117
  MALE                 75                208
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    84  21
  19P LOSS WILD-TYPE 238  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     84   21
  19P LOSS WILD-TYPE  238   55
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                84                238
  YES               21                 55
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  19P LOSS MUTATED                                          2
  19P LOSS WILD-TYPE                                       11
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  19P LOSS MUTATED                                      10
  19P LOSS WILD-TYPE                                    62
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                       40
  19P LOSS WILD-TYPE                                                    123
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  19P LOSS MUTATED                                                   1
  19P LOSS WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                                  31
  19P LOSS WILD-TYPE                                                                51
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  19P LOSS MUTATED                                                    4
  19P LOSS WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  19P LOSS MUTATED                                                 28
  19P LOSS WILD-TYPE                                               51
D75V9, multiclass
                                                                   clus
vv                                                                  19P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           10
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          40
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               31
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                28
                                                                   clus
vv                                                                  19P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             62
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           123
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 51
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  51
[1] 7 2
[1] TRUE
[1] "dimension of 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    92   1   6   4
  19P LOSS WILD-TYPE 257  17  13  21
D75V10, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               92                257
  R1                1                 17
  R2                6                 13
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED      26                         5
  19P LOSS WILD-TYPE    62                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           1    66
  19P LOSS WILD-TYPE                                         0   212
D75V12, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                                   26                 62
  BLACK OR AFRICAN AMERICAN                                5                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   66                212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V13, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1  78
  19P LOSS WILD-TYPE   4 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   78
  19P LOSS WILD-TYPE    4  238
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               78                238
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    50  32
  19Q LOSS WILD-TYPE 196 137
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                82                333 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                32                137 
$`19Q LOSS MUTATED`
TCGA-VQ-A8PU TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6565 
       27.35        11.01         9.44         6.61         9.67         9.17 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 
       35.24        33.63        28.73        11.44         0.69         2.66 
TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8678 TCGA-BR-A4CS TCGA-BR-A4PD 
        2.20        14.04        14.79        24.79         1.48        20.65 
TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8527 
        1.15        13.02        13.15        12.10        12.59         7.17 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4440 
        6.31        11.31        12.43        12.20        20.02         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 
       29.98        19.07        18.97        12.03        15.02        69.04 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A6EX 
       10.26        15.22        12.79        11.31        19.50        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 
       22.29        15.65         0.62        17.06         0.56         5.92 
TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H5 
       18.15        11.77         8.98         6.58        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       21.17        33.40        18.38        12.59        10.62        11.70 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BW TCGA-RD-A8MW 
        5.56        37.64        45.67        18.21         5.13        37.91 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PK 
       48.79         5.46        13.02        18.48        43.36        17.85 
TCGA-VQ-A8PM TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
        1.87        18.74        42.64         9.50        55.56         9.04 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       38.93        17.13        27.55         0.79 

$`19Q LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       20.15         9.86        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       44.94        21.90         9.21        36.16        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       37.25        14.43        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.56        29.42        19.96        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
       26.33         4.31         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42        21.44        16.14         5.13        13.41 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 
       13.18        13.35        11.21        12.76        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       12.82        12.43        12.30        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        8.05        54.08        14.01        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       13.35        17.19        15.98        12.36        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.24        11.44        20.32         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       11.38         3.48        19.53        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51        26.47         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        2.10        12.95        29.00        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.44         6.74         6.51        15.75        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF 
       63.62        36.95         3.72        19.73        14.04         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       57.44         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        0.92        13.25        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        12.79         2.70         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        21.83        61.22        20.81        32.88         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       60.85         9.73         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        5.72        66.81        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        12.43        17.26 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.56               0.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             69.04             122.30 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             13.02              15.65 
[1] "0.6 - 69.0 (13.0)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         1        4        8        6        10        11
  19Q LOSS WILD-TYPE       1       12       33       26        30        45
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           0         16         12          5       10
  19Q LOSS WILD-TYPE         3         65         51         34       34
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  4                 12
  STAGE IB                  8                 33
  STAGE II                  6                 26
  STAGE IIA                10                 30
  STAGE IIB                11                 45
  STAGE III                 0                  3
  STAGE IIIA               16                 65
  STAGE IIIB               12                 51
  STAGE IIIC                5                 34
  STAGE IV                 10                 34
[1] 11  2
[1] 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     5  18  39  22
  19Q LOSS WILD-TYPE  18  75 157  97
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                5                 18
  T2               18                 75
  T3               39                157
  T4               22                 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"
                    vv
clus                  N0  N1  N2  N3
  19Q LOSS MUTATED    27  19  17  19
  19Q LOSS WILD-TYPE 103 100  69  69
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               27                103
  N1               19                100
  N2               17                 69
  N3               19                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    77   6
  19Q LOSS WILD-TYPE 312  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     77    6
  19Q LOSS WILD-TYPE  312   24
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               77                312
  1                6                 24
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    31  55
  19Q LOSS WILD-TYPE 127 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     31   55
  19Q LOSS WILD-TYPE  127  228
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               31                127
  MALE                 55                228
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    63  15
  19Q LOSS WILD-TYPE 259  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     63   15
  19Q LOSS WILD-TYPE  259   61
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                63                259
  YES               15                 61
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  19Q LOSS MUTATED                                          2
  19Q LOSS WILD-TYPE                                       11
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  19Q LOSS MUTATED                                       6
  19Q LOSS WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                       28
  19Q LOSS WILD-TYPE                                                    135
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  19Q LOSS MUTATED                                                   2
  19Q LOSS WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                                  21
  19Q LOSS WILD-TYPE                                                                61
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  19Q LOSS MUTATED                                                    4
  19Q LOSS WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  19Q LOSS MUTATED                                                 23
  19Q LOSS WILD-TYPE                                               56
D76V9, multiclass
                                                                   clus
vv                                                                  19Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          28
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               21
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                23
                                                                   clus
vv                                                                  19Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           135
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 61
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  56
[1] 7 2
[1] TRUE
[1] "dimension of 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    70   0   4   3
  19Q LOSS WILD-TYPE 279  18  15  22
D76V10, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               70                279
  R1                0                 18
  R2                4                 15
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19Q LOSS MUTATED      21                         3
  19Q LOSS WILD-TYPE    67                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           0    47
  19Q LOSS WILD-TYPE                                         1   231
D76V12, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                                   21                 67
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   47                231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V13, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  58
  19Q LOSS WILD-TYPE   4 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   58
  19Q LOSS WILD-TYPE    4  258
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               58                258
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    10  10
  20P LOSS WILD-TYPE 236 159
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                20                395 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                10                159 
$`20P LOSS MUTATED`
TCGA-EQ-A4SO TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-8289 TCGA-BR-A4PD 
       16.24         6.18        17.29        26.10         2.66        20.65 
TCGA-CG-4301 TCGA-D7-6519 TCGA-D7-8575 TCGA-D7-8576 TCGA-EQ-5647 TCGA-HF-7133 
        3.02        20.55        18.21        14.66         0.62        63.06 
TCGA-HU-8249 TCGA-IN-A6RJ TCGA-IN-AB1V TCGA-IP-7968 TCGA-VQ-A8DU TCGA-VQ-A8E0 
       28.96        12.46        15.75         2.53         5.46        18.48 
TCGA-VQ-A8PY TCGA-VQ-AA68 
       14.33        43.66 

$`20P LOSS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        9.86        27.35        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         9.67         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       13.87        13.68        19.33        39.12         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 
       12.33        24.72        16.80        19.50        17.19        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       30.51        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       36.36         3.45        18.81         3.39        18.38        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       11.70        13.51         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        29.59        64.57        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.62               0.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             63.06             122.30 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            15.995             14.760 
[1] "0.6 - 63.1 (16.0)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.4"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         0        3        2        0         0         2
  20P LOSS WILD-TYPE       2       13       39       32        40        54
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           0          5          4          1        4
  20P LOSS WILD-TYPE         3         76         59         38       40
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 13
  STAGE IB                  2                 39
  STAGE II                  0                 32
  STAGE IIA                 0                 40
  STAGE IIB                 2                 54
  STAGE III                 0                  3
  STAGE IIIA                5                 76
  STAGE IIIB                4                 59
  STAGE IIIC                1                 38
  STAGE IV                  4                 40
[1] 11  2
[1] 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     3   4   9   6
  20P LOSS WILD-TYPE  20  89 187 113
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                3                 20
  T2                4                 89
  T3                9                187
  T4                6                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P LOSS MUTATED     6   4   7   5
  20P LOSS WILD-TYPE 124 115  79  83
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                6                124
  N1                4                115
  N2                7                 79
  N3                5                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    16   3
  20P LOSS WILD-TYPE 373  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     16    3
  20P LOSS WILD-TYPE  373   27
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               16                373
  1                3                 27
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    11  11
  20P LOSS WILD-TYPE 147 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     11   11
  20P LOSS WILD-TYPE  147  272
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               11                147
  MALE                 11                272
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    12   8
  20P LOSS WILD-TYPE 310  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12    8
  20P LOSS WILD-TYPE  310   68
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                12                310
  YES                8                 68
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  20P LOSS MUTATED                                          0
  20P LOSS WILD-TYPE                                       13
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  20P LOSS MUTATED                                       2
  20P LOSS WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                       10
  20P LOSS WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  20P LOSS MUTATED                                                   1
  20P LOSS WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                                   2
  20P LOSS WILD-TYPE                                                                80
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  20P LOSS MUTATED                                                    0
  20P LOSS WILD-TYPE                                                  8
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  20P LOSS MUTATED                                                  6
  20P LOSS WILD-TYPE                                               73
D77V9, multiclass
                                                                   clus
vv                                                                  20P LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 6
                                                                   clus
vv                                                                  20P LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          13
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 80
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  73
[1] 7 2
[1] TRUE
[1] "dimension of 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    18   1   2   1
  20P LOSS WILD-TYPE 331  17  17  24
D77V10, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               18                331
  R1                1                 17
  R2                2                 17
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20P LOSS MUTATED       2                         1
  20P LOSS WILD-TYPE    86                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           0    16
  20P LOSS WILD-TYPE                                         1   262
D77V12, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                                    2                 86
  BLACK OR AFRICAN AMERICAN                                1                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   16                262
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  15
  20P LOSS WILD-TYPE   5 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   15
  20P LOSS WILD-TYPE    5  301
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               15                301
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   102  70
  21Q LOSS WILD-TYPE 144  99
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               172                243 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                70                 99 
$`21Q LOSS MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       47.05        22.98         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4191 
       26.93        11.70        11.01         9.44         6.97        18.35 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
        4.08         9.67        13.68        19.33        26.10         9.17 
TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 
       31.20        35.24        33.63        39.78        28.73        33.21 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8296 
       14.43        11.44         9.60         8.05        19.96        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 
        7.40        31.10        17.52         4.31        14.04        14.79 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 
        5.39        25.18         9.21        24.79         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 
       10.68         7.53        34.98         1.48         0.72        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 
        0.46        20.65        20.42         1.15        21.44        12.76 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A489 
       12.53         7.17        12.33        12.39        12.82        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 
       12.43        11.61        12.20        20.02        54.08         4.01 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 
       12.03        18.97        30.97         6.97         1.02        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 
       15.02        65.10         4.01        69.04        20.91        19.13 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8576 
       13.35        17.19        15.98        12.79        11.31        14.66 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       21.14        16.44        11.31        15.65        19.96         0.62 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A9TM TCGA-HF-7133 
       72.23        11.38        19.53        17.06         6.21        63.06 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GC 
       26.47         1.51        28.96        22.82        22.68         3.25 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        8.98         6.58         0.26        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.17        36.36        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
       13.35         6.74         6.51        10.62        11.70        15.75 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 
        2.53         5.56        63.62        37.64        36.95        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 
       45.67        18.21         8.52        74.53         6.08         9.24 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      122.30        37.91       115.69        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8P5 
        5.79         0.92        48.79        13.25        18.48         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PX TCGA-VQ-A8PY 
       22.19        17.85         1.87        23.41        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       39.45        61.22        18.74        20.81         1.71        42.64 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A94O 
        9.73        55.56         2.01        55.43         4.54        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       42.54        11.24        18.41        43.66        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       54.12        27.55        12.43         0.79 

$`21Q LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI 
       21.99        79.07        16.24        58.03        26.70        19.56 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        9.47         6.61         4.64         7.43        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.87        17.29        39.12        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        30.90        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       21.90         9.21        36.16        35.84        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 
        3.45         9.07        29.56        37.25         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 
       32.25         0.56        29.42         2.66         2.20         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 
       13.08         0.26        22.19         0.95        26.33         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 
       11.80        31.27         7.36        25.05         3.72        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T 
        7.53        26.73        31.96        32.58         8.22        34.13 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       13.87         6.08        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL 
       14.17         0.53        28.34         0.66        32.52        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       11.21        12.10        12.59        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG 
       15.39        12.07        12.43         6.31        12.30         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
        7.99         8.05        14.01        29.98        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
        9.01         7.07        12.00        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
        0.99       105.07        28.96        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       10.26        15.22        12.36        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       19.50        17.19        18.21        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
       20.32        22.29         8.38         4.34         7.13         7.99 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       14.47        21.27         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7134 
        5.03        13.58         0.56         5.52        77.29        52.21 
TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       30.51         5.92        24.39        18.15        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD 
        0.76        24.30         5.59        24.26        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       20.25         2.10        12.95        14.07        15.68        33.40 
TCGA-IN-7808 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-AB1X TCGA-MX-A5UG 
        3.45        19.53         6.44        12.59        13.51         3.72 
TCGA-MX-A5UJ TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       19.73         4.60        11.05         8.61         5.13        16.67 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DU 
       40.64       116.38        71.38        16.87        19.04         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ 
        2.70         9.27        15.65        13.35        29.59        73.41 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 
       11.70        21.83        32.88        60.85         9.50         9.04 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6A 
        6.58         5.72        66.81         2.66        28.41        38.93 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       26.04        16.14        17.26 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.23               0.00 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            122.30             116.38 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            15.615             14.270 
[1] "0.2 - 122.3 (15.6)" "0.0 - 116.4 (14.3)"
[1] "hr=" "1.1"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         1        5       17        9        17        23
  21Q LOSS WILD-TYPE       1       11       24       23        23        33
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           2         41         26         15       16
  21Q LOSS WILD-TYPE         1         40         37         24       28
D78V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  5                 11
  STAGE IB                 17                 24
  STAGE II                  9                 23
  STAGE IIA                17                 23
  STAGE IIB                23                 33
  STAGE III                 2                  1
  STAGE IIIA               41                 40
  STAGE IIIB               26                 37
  STAGE IIIC               15                 24
  STAGE IV                 16                 28
[1] 11  2
[1] 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     7  39  85  45
  21Q LOSS WILD-TYPE  16  54 111  74
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                7                 16
  T2               39                 54
  T3               85                111
  T4               45                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  21Q LOSS MUTATED   46 52 40 35
  21Q LOSS WILD-TYPE 84 67 46 53
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               46                 84
  N1               52                 67
  N2               40                 46
  N3               35                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   163   9
  21Q LOSS WILD-TYPE 226  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    163    9
  21Q LOSS WILD-TYPE  226   21
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              163                226
  1                9                 21
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    70 111
  21Q LOSS WILD-TYPE  88 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     70  111
  21Q LOSS WILD-TYPE   88  172
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               70                 88
  MALE                111                172
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   128  37
  21Q LOSS WILD-TYPE 194  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    128   37
  21Q LOSS WILD-TYPE  194   39
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO               128                194
  YES               37                 39
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  21Q LOSS MUTATED                                          6
  21Q LOSS WILD-TYPE                                        7
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  21Q LOSS MUTATED                                      24
  21Q LOSS WILD-TYPE                                    48
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                       63
  21Q LOSS WILD-TYPE                                                    100
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  21Q LOSS MUTATED                                                   9
  21Q LOSS WILD-TYPE                                                12
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                                  39
  21Q LOSS WILD-TYPE                                                                43
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  21Q LOSS MUTATED                                                    1
  21Q LOSS WILD-TYPE                                                  7
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  21Q LOSS MUTATED                                                 38
  21Q LOSS WILD-TYPE                                               41
D78V9, multiclass
                                                                   clus
vv                                                                  21Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           24
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          63
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                38
                                                                   clus
vv                                                                  21Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             48
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           100
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 12
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 43
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  41
[1] 7 2
[1] TRUE
[1] "dimension of 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   147   7   6   8
  21Q LOSS WILD-TYPE 202  11  13  17
D78V10, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              147                202
  R1                7                 11
  R2                6                 13
  RX                8                 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"
D78V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  21Q LOSS MUTATED      31                         6
  21Q LOSS WILD-TYPE    57                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           0   114
  21Q LOSS WILD-TYPE                                         1   164
D78V12, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                                   31                 57
  BLACK OR AFRICAN AMERICAN                                6                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  114                164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     2 121
  21Q LOSS WILD-TYPE   3 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2  121
  21Q LOSS WILD-TYPE    3  195
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              121                195
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    81  59
  22Q LOSS WILD-TYPE 165 110
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               140                275 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                59                110 
$`22Q LOSS MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       47.05        21.99        16.24        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 
       26.93        58.03        11.01         9.44         6.61         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
        9.67         6.18        17.29        19.33        26.10         9.17 
TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-8058 TCGA-BR-8059 
       12.16         9.21        33.63        39.78        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8484 
       11.44         0.69         9.60         7.40        14.04        25.18 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       26.73        24.79        32.58         9.86         8.22        10.68 
TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
       34.98         0.72        32.52        20.65         1.15        21.44 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 
       13.15        13.35        12.76        12.53         7.17        12.39 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       15.39        12.07         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 
       11.61        12.20         8.05        54.08         4.01        18.97 
TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 
       30.97        12.03        15.02        69.04        12.66        20.91 
TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 
       20.55        10.26        15.22        12.79        11.31        19.50 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A 
       18.21        21.14        16.44        11.31        15.65        19.96 
TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
        0.62        19.53        17.06         0.56         5.52         6.21 
TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GY 
       63.06         5.92        28.96        22.75         8.98         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI 
        2.10        23.84        21.17        33.40         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V 
       12.46        19.53         6.44         6.74        11.70        15.75 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        2.53         5.56        36.95        14.04        45.67        18.21 
TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB 
        6.08         8.61        16.67       115.69        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        0.92        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PY 
       46.26        22.19        12.79        17.85         1.87        14.33 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       39.45        18.74        20.81         1.71        42.64         9.50 
TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A 
        9.73         4.54        66.81        11.24        18.41        38.93 
TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       32.94         0.79 

$`22Q LOSS WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       22.98        79.07         0.23        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.87        13.68        39.12        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       21.90        36.16        35.24        35.84        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8078 
       28.73         3.45         9.07        29.56        33.21        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8686 
        9.34        28.14         6.28         7.53        31.96        20.88 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        13.51         0.46        20.42        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 
       13.41        13.02        13.18        11.21        12.10        12.59 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
       12.33        12.30        12.59        11.64        12.82        12.43 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
       15.95         1.02         7.99        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
       12.03         0.00         9.01         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       17.19        15.98        12.36        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       17.19        14.66        20.91        14.27         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
       22.29         8.38         4.34         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
       59.54         5.03        13.58        77.29        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51         6.58        20.25        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       23.80        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 
       13.35        12.59         6.51        10.62        13.51        63.62 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       37.64         3.72        19.73         8.52        74.53         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        9.24        11.05         5.13       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       30.97        34.29        16.31         2.50         2.70         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       23.41        15.65        13.35        29.59        64.57        73.41 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Z 
       11.70        21.83        61.22        32.88        60.85        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
        9.04         2.01        55.43         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F 
        2.66        42.54        43.66        28.41        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.26               0.00 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            115.69             122.30 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            13.695             15.680 
[1] "0.3 - 115.7 (13.7)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.2"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         1        2       15       12        13        18
  22Q LOSS WILD-TYPE       1       14       26       20        27        38
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           2         32         23         10       13
  22Q LOSS WILD-TYPE         1         49         40         29       31
D79V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  2                 14
  STAGE IB                 15                 26
  STAGE II                 12                 20
  STAGE IIA                13                 27
  STAGE IIB                18                 38
  STAGE III                 2                  1
  STAGE IIIA               32                 49
  STAGE IIIB               23                 40
  STAGE IIIC               10                 29
  STAGE IV                 13                 31
[1] 11  2
[1] 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     6  32  73  33
  22Q LOSS WILD-TYPE  17  61 123  86
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                6                 17
  T2               32                 61
  T3               73                123
  T4               33                 86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  22Q LOSS MUTATED   39 34 35 31
  22Q LOSS WILD-TYPE 91 85 51 57
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               39                 91
  N1               34                 85
  N2               35                 51
  N3               31                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   132   6
  22Q LOSS WILD-TYPE 257  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    132    6
  22Q LOSS WILD-TYPE  257   24
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              132                257
  1                6                 24
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    49  97
  22Q LOSS WILD-TYPE 109 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     49   97
  22Q LOSS WILD-TYPE  109  186
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               49                109
  MALE                 97                186
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   105  32
  22Q LOSS WILD-TYPE 217  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    105   32
  22Q LOSS WILD-TYPE  217   44
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               105                217
  YES               32                 44
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  22Q LOSS MUTATED                                          6
  22Q LOSS WILD-TYPE                                        7
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  22Q LOSS MUTATED                                      18
  22Q LOSS WILD-TYPE                                    54
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                       52
  22Q LOSS WILD-TYPE                                                    111
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  22Q LOSS MUTATED                                                   8
  22Q LOSS WILD-TYPE                                                13
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                                  25
  22Q LOSS WILD-TYPE                                                                57
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  22Q LOSS MUTATED                                                    2
  22Q LOSS WILD-TYPE                                                  6
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  22Q LOSS MUTATED                                                 34
  22Q LOSS WILD-TYPE                                               45
D79V9, multiclass
                                                                   clus
vv                                                                  22Q LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           18
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          52
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               25
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                34
                                                                   clus
vv                                                                  22Q LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             54
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           111
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 57
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  45
[1] 7 2
[1] TRUE
[1] "dimension of 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   111   8   8   6
  22Q LOSS WILD-TYPE 238  10  11  19
D79V10, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0              111                238
  R1                8                 10
  R2                8                 11
  RX                6                 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"
D79V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  22Q LOSS MUTATED      29                         3
  22Q LOSS WILD-TYPE    59                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           1    93
  22Q LOSS WILD-TYPE                                         0   185
D79V12, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                                   29                 59
  BLACK OR AFRICAN AMERICAN                                3                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   93                185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     2 100
  22Q LOSS WILD-TYPE   3 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2  100
  22Q LOSS WILD-TYPE    3  216
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              100                216
[1] 2 2
[1] FALSE

Clustering(80) Variable = XP LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    39  20
  XP LOSS WILD-TYPE 207 149
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               59               356 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               20               149 
$`XP LOSS MUTATED`
TCGA-CG-4444 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TN 
       47.05        27.35        26.93        58.03        19.56         9.44 
TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-7703 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8361 
       18.35        19.33        36.16        19.96         7.40        31.10 
TCGA-BR-8362 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4PF TCGA-BR-A4QI 
       13.08         9.86        13.87        34.98         1.15        21.44 
TCGA-CD-8524 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH 
       12.76        11.64        12.07        12.82        11.31        12.20 
TCGA-CG-4301 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-5579 
        3.02        29.98        19.07         7.07        15.02        20.91 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX 
       15.22        15.98        12.79        12.33        18.21        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-8604 
       20.32        15.65        19.96        13.58         5.52        22.82 
TCGA-HU-A4GD TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       22.75        23.80        36.36         3.39        18.38        13.35 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-KB-A93J TCGA-R5-A7O7 TCGA-VQ-A8PC TCGA-VQ-A8PS 
        6.44         6.74        36.95        45.67        46.26        13.35 
TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       55.56        66.81        43.66        38.93        17.13 

$`XP LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
        9.86        26.70        11.70        11.01         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       32.25         8.05         0.56        29.42         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       15.58         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 
       32.58        20.88         8.22        10.68        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.65        20.42        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.10        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       12.39        12.59        15.39        12.43         6.31        12.30 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        11.77        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
        4.01        14.01        12.03         0.00         9.01        18.97 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       13.35        17.19        10.26        12.36        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.24        11.44        22.29         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       59.54         5.03         0.56         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       18.15        28.96        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        24.26        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       23.84        21.17        14.07        15.68        33.40         3.45 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       18.81        12.46        19.53        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       37.64         3.72        19.73        14.04        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       37.22         7.73        30.97        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       39.45        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
       21.04         2.66        42.54        11.24        18.41        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             1.15              0.00 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            66.81            122.30 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            18.21             14.30 
[1] "1.1 - 66.8 (18.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D80V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED         1        2        7        5         4         9
  XP LOSS WILD-TYPE       1       14       34       27        36        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED           0         17          4          7        3
  XP LOSS WILD-TYPE         3         64         59         32       41
D80V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 2                14
  STAGE IB                 7                34
  STAGE II                 5                27
  STAGE IIA                4                36
  STAGE IIB                9                47
  STAGE III                0                 3
  STAGE IIIA              17                64
  STAGE IIIB               4                59
  STAGE IIIC               7                32
  STAGE IV                 3                41
[1] 11  2
[1] 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     4  15  27  14
  XP LOSS WILD-TYPE  19  78 169 105
D80V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               4                19
  T2              15                78
  T3              27               169
  T4              14               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XP LOSS MUTATED    18  19  13   9
  XP LOSS WILD-TYPE 112 100  73  79
D80V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              18               112
  N1              19               100
  N2              13                73
  N3               9                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    56   2
  XP LOSS WILD-TYPE 333  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     56    2
  XP LOSS WILD-TYPE  333   28
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              56               333
  1               2                28
[1] 2 2
[1] FALSE
D80V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    15  46
  XP LOSS WILD-TYPE 143 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     15   46
  XP LOSS WILD-TYPE  143  237
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              15               143
  MALE                46               237
[1] 2 2
[1] FALSE
D80V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    44  13
  XP LOSS WILD-TYPE 278  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     44   13
  XP LOSS WILD-TYPE  278   63
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               44               278
  YES              13                63
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  XP LOSS MUTATED                                          3
  XP LOSS WILD-TYPE                                       10
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  XP LOSS MUTATED                                       8
  XP LOSS WILD-TYPE                                    64
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XP LOSS MUTATED                                                       22
  XP LOSS WILD-TYPE                                                    141
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  XP LOSS MUTATED                                                   2
  XP LOSS WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XP LOSS MUTATED                                                                   6
  XP LOSS WILD-TYPE                                                                76
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  XP LOSS MUTATED                                                    2
  XP LOSS WILD-TYPE                                                  6
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  XP LOSS MUTATED                                                 18
  XP LOSS WILD-TYPE                                               61
D80V9, multiclass
                                                                   clus
vv                                                                  XP LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               18
                                                                   clus
vv                                                                  XP LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                76
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of 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    47   4   1   2
  XP LOSS WILD-TYPE 302  14  18  23
D80V10, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              47               302
  R1               4                14
  R2               1                18
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XP LOSS MUTATED      10                         0
  XP LOSS WILD-TYPE    78                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP LOSS MUTATED                                           0    44
  XP LOSS WILD-TYPE                                         1   234
D80V12, multiclass
                                           clus
vv                                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                                  10                78
  BLACK OR AFRICAN AMERICAN                               0                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  44               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2  43
  XP LOSS WILD-TYPE   3 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   43
  XP LOSS WILD-TYPE    3  273
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              43               273
[1] 2 2
[1] FALSE

Clustering(81) Variable = XQ LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    34  20
  XQ LOSS WILD-TYPE 212 149
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               54               361 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               20               149 
$`XQ LOSS MUTATED`
TCGA-CG-4444 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TN 
       47.05        27.35        26.93        58.03        19.56         9.44 
TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-8291 TCGA-BR-8361 
       18.35        19.33         9.21        36.16        19.96        31.10 
TCGA-BR-8678 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4PF TCGA-BR-A4QI 
       24.79        13.87        34.98         1.48         1.15        21.44 
TCGA-CD-8524 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 TCGA-CG-4301 
       12.76        11.64        12.07        12.82        11.31         3.02 
TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-5579 
        7.99        29.98        19.07         7.07        15.02        20.91 
TCGA-D7-6519 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX 
       20.55        12.79        12.33        18.21        14.66        11.31 
TCGA-D7-A6EZ TCGA-D7-A74A TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8604 
       20.32        19.96        13.58         5.52        63.06        22.82 
TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RR 
       23.80        36.36         3.39        18.38         6.44         6.74 
TCGA-KB-A93J TCGA-VQ-A8E0 TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-AA6A TCGA-VQ-AA6D 
       36.95        18.48        13.35        20.81        38.93        17.13 

$`XQ LOSS WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
        9.86        26.70        11.70        11.01         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        7.53         6.08        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.65        20.42        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.10        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       12.39        12.59        15.39        12.43         6.31        12.30 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
       20.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
        4.01        14.01        12.03         0.00         9.01        18.97 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        12.36        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        19.50        17.19        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.24        11.44        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 
       17.06        59.54         5.03         0.56         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       18.15        28.96        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        21.17        14.07        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
        3.45        18.81        12.46        13.35        19.53        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        37.64         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.25        13.02        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        18.74        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B 
       42.54        11.24        18.41        43.66        28.41        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             1.15              0.00 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            63.06            122.30 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           18.365            14.330 
[1] "1.1 - 63.1 (18.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         1        2        6        6         3         7
  XQ LOSS WILD-TYPE       1       14       35       26        37        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           0         15          3          5        4
  XQ LOSS WILD-TYPE         3         66         60         34       40
D81V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 2                14
  STAGE IB                 6                35
  STAGE II                 6                26
  STAGE IIA                3                37
  STAGE IIB                7                49
  STAGE III                0                 3
  STAGE IIIA              15                66
  STAGE IIIB               3                60
  STAGE IIIC               5                34
  STAGE IV                 4                40
[1] 11  2
[1] 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     4  14  25  11
  XQ LOSS WILD-TYPE  19  79 171 108
D81V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               4                19
  T2              14                79
  T3              25               171
  T4              11               108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ LOSS MUTATED    17  15  11  10
  XQ LOSS WILD-TYPE 113 104  75  78
D81V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              17               113
  N1              15               104
  N2              11                75
  N3              10                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    52   1
  XQ LOSS WILD-TYPE 337  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     52    1
  XQ LOSS WILD-TYPE  337   29
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              52               337
  1               1                29
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    13  42
  XQ LOSS WILD-TYPE 145 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13   42
  XQ LOSS WILD-TYPE  145  241
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              13               145
  MALE                42               241
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    37  14
  XQ LOSS WILD-TYPE 285  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     37   14
  XQ LOSS WILD-TYPE  285   62
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               37               285
  YES              14                62
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  XQ LOSS MUTATED                                          2
  XQ LOSS WILD-TYPE                                       11
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  XQ LOSS MUTATED                                       8
  XQ LOSS WILD-TYPE                                    64
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                       21
  XQ LOSS WILD-TYPE                                                    142
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  XQ LOSS MUTATED                                                   3
  XQ LOSS WILD-TYPE                                                18
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                                   8
  XQ LOSS WILD-TYPE                                                                74
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  XQ LOSS MUTATED                                                    2
  XQ LOSS WILD-TYPE                                                  6
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  XQ LOSS MUTATED                                                 11
  XQ LOSS WILD-TYPE                                               68
D81V9, multiclass
                                                                   clus
vv                                                                  XQ LOSS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         21
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               11
                                                                   clus
vv                                                                  XQ LOSS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                74
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 68
[1] 7 2
[1] TRUE
[1] "dimension of 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    43   5   1   2
  XQ LOSS WILD-TYPE 306  13  18  23
D81V10, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              43               306
  R1               5                13
  R2               1                18
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XQ LOSS MUTATED       7                         1
  XQ LOSS WILD-TYPE    81                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           0    37
  XQ LOSS WILD-TYPE                                         1   241
D81V12, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                                   7                81
  BLACK OR AFRICAN AMERICAN                               1                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  37               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V13, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1  38
  XQ LOSS WILD-TYPE   4 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   38
  XQ LOSS WILD-TYPE    4  278
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              38               278
[1] 2 2
[1] FALSE
