[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/15090008/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/15098845/transformed.cor.cli.txt"

nPatients in clinical file=438, in cluster file=441, common to both=436
[1] "Reduce the number of clustering variables from 82 to 81."
[1]  81 436
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               51               385 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               51               385 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              103               333 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              103               333 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               76               360 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               76               360 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               65               371 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               65               371 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               53               383 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               53               383 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               93               343 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               93               343 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               21               415 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               21               415 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               420 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               420 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              100               336 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              100               336 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               43               393 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               43               393 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               76               360 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               76               360 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               62               374 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               62               374 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              196               240 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              196               240 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              168               268 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              168               268 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              180               256 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              180               256 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              234               202 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              234               202 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               59               377 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               59               377 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               77               359 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               77               359 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                98                338 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                98                338 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                70                366 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                70                366 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                64                372 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                64                372 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                74                362 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                74                362 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                89                347 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                89                347 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                76                360 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                76                360 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               153                283 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               153                283 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                29                407 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                29                407 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                39                397 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                39                397 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                59                377 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                59                377 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                47                389 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                47                389 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                28                408 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                28                408 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                60                376 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                60                376 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                82                354 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                82                354 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                53                383 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                53                383 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                53                383 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                53                383 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                76                360 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                76                360 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               240                196 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               240                196 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               276                160 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               276                160 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                415 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                415 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                32                404 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                32                404 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               48               388 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               48               388 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               55               381 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               55               381 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               59               377 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               59               377 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               408 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               408 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               26               410 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               26               410 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               33               403 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               33               403 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               89               347 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               89               347 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               54               382 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               54               382 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              165               271 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              165               271 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              162               274 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              162               274 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               59               377 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               59               377 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              105               331 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              105               331 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               52               384 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               52               384 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               69               367 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               69               367 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               20               416 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               20               416 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               30               406 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               30               406 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               85               351 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               85               351 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               33               403 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               33               403 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              146               290 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              146               290 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              102               334 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              102               334 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                64                372 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                64                372 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                67                369 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                67                369 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                62                374 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                62                374 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                60                376 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                60                376 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                61                375 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                61                375 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                52                384 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                52                384 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                35                401 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                35                401 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               110                326 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               110                326 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                89                347 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                89                347 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                99                337 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                99                337 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               114                322 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               114                322 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               161                275 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               161                275 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                74                362 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                74                362 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               117                319 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               117                319 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               153                283 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               153                283 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               114                322 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               114                322 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                87                349 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                87                349 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                22                414 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                22                414 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               177                259 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               177                259 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               142                294 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               142                294 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               56               380 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               56               380 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               48               388 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               48               388 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "COMPLETENESS_OF_RESECTION"             
[17] "NUMBER_OF_LYMPH_NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 436 columns.

[1] "Batch" "20"   
[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=137,	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=247,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=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:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH_NUMBER':	nDistinctValues=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 436 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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "COMPLETENESS_OF_RESECTION"             
[10] "NUMBER_OF_LYMPH_NODES"                 
[11] "RACE"                                  
[12] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=54, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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 
 22  90 195 119 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 22  90 195 119 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 22  90 195 119 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 22  90 195 119 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
129 118  84  89 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
129 118  84  89 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
129 118  84  89 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
129 118  84  89 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=7, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=34, 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    25  20
  1P GAIN WILD-TYPE 229 130
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               45               359 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               20               130 
$`1P GAIN MUTATED`
TCGA-BR-4267 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8381 TCGA-BR-8483 
        6.18        18.15         3.45        12.95         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-CD-8535 
       25.18        12.79         8.22         0.72        13.51         0.13 
TCGA-CD-A48A TCGA-CG-4436 TCGA-D7-6521 TCGA-D7-6820 TCGA-D7-A4YU TCGA-D7-A6F0 
       12.43         7.99        18.54        11.31        16.44         2.96 
TCGA-EQ-8122 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4GF TCGA-HU-A4GH 
        7.99         5.52        26.47         5.92        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RO 
        8.98         6.25        12.95         3.45        18.38         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-KB-A6F7 TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 
        6.44         6.74        60.56         6.08        16.67       115.69 
TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PK TCGA-VQ-A8PZ 
        8.94        48.79        18.48        35.24        17.85        65.16 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A 
       42.54        18.41        32.94 

$`1P GAIN WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       35.24        23.93        15.42        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56         2.66        16.31         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        19.50        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-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 
       19.17        14.79        15.85         3.72         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82         0.66        19.36         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        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
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         0.10        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-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        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        12.36        12.66        11.93        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-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       13.71        11.24        11.31        11.44         9.76        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
        8.38         4.34         7.40         7.13         0.62        16.24 
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-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        0.56         0.23        18.08         1.51        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
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        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.81        27.42        21.21        18.81         3.39         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        5.19        13.08        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H 
        7.82        13.51         2.53         5.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73         9.86        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       61.25         4.60         9.24        11.05         8.61         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-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       35.61        16.87        19.04         5.79         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        28.96        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       36.69        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       22.68         1.71        36.16         7.36         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       52.24         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U 
        5.72        64.18        21.04         2.66        11.24        22.09 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       40.08        28.41        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.13              0.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           115.69            122.30 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            12.43             12.89 
[1] "0.1 - 115.7 (12.4)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         1        2        7        2         4         6
  1P GAIN WILD-TYPE       2       12       34       29        34        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           2          9          8          5        2
  1P GAIN WILD-TYPE         2         76         54         36       44
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 2                12
  STAGE IB                 7                34
  STAGE II                 2                29
  STAGE IIA                4                34
  STAGE IIB                6                49
  STAGE III                2                 2
  STAGE IIIA               9                76
  STAGE IIIB               8                54
  STAGE IIIC               5                36
  STAGE IV                 2                44
[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  10  25   9
  1P GAIN WILD-TYPE  17  80 170 110
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               5                17
  T2              10                80
  T3              25               170
  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
  1P GAIN MUTATED    15  12  10  10
  1P GAIN WILD-TYPE 114 106  74  79
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              15               114
  N1              12               106
  N2              10                74
  N3              10                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    47   1
  1P GAIN WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     47    1
  1P GAIN WILD-TYPE  340   29
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              47               340
  1               1                29
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    15  36
  1P GAIN WILD-TYPE 143 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     15   36
  1P GAIN WILD-TYPE  143  242
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              15               143
  MALE                36               242
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1P GAIN MUTATED                                       6
  1P GAIN WILD-TYPE                                    65
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                       22
  1P GAIN WILD-TYPE                                                    140
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                                  12
  1P GAIN WILD-TYPE                                                                69
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  1P GAIN MUTATED                                                  8
  1P GAIN WILD-TYPE                                               70
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  1P GAIN MUTATED                                                          0
  1P GAIN WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  1P GAIN MUTATED                                                           0
  1P GAIN WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  1P GAIN MUTATED                                          3
  1P GAIN WILD-TYPE                                       10
D1V8, multiclass
                                                                   clus
vv                                                                  1P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  1P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 70
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         10
[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"
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  51
  1P GAIN WILD-TYPE   6 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   51
  1P GAIN WILD-TYPE    6  379
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                 6
  YES              51               379
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    40   3   0   4
  1P GAIN WILD-TYPE 307  15  19  21
D1V10, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              40               307
  R1               3                15
  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                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           0    35
  1P GAIN WILD-TYPE                                         1   239
D1V12, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  35               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"
D1V13, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  41
  1P GAIN WILD-TYPE   4 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   41
  1P GAIN WILD-TYPE    4  272
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              41               272
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    55  38
  1Q GAIN WILD-TYPE 199 112
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               93               311 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               38               112 
$`1Q GAIN MUTATED`
TCGA-B7-A5TJ TCGA-BR-4267 TCGA-BR-6705 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 
       11.01         6.18        25.61        18.15        28.73         3.45 
TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8483 
       12.95         2.20         6.18        14.04         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE 
        8.22         7.53         0.72        12.82        13.51        20.42 
TCGA-BR-A4PF TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A48C 
        1.15         0.07         0.16         0.13         0.13        11.61 
TCGA-CD-A4MG TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4460 TCGA-D7-5578 TCGA-D7-5579 
        6.58         7.99        54.08        21.99        12.66        11.93 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       18.54        17.19        10.26        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 
       12.33        24.72        19.50        16.44        11.31         2.96 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8211 
        0.62         7.99        72.23         3.48        14.07        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        14.27        14.17 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H2 
       25.81        11.77         8.98         0.10         6.25        12.95 
TCGA-IN-7808 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        3.45         1.41         6.44        60.56        18.21         6.08 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.67       115.69         8.94        35.61        48.79         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       18.48        35.24         2.70        17.85        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91S TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
       36.69        22.68        64.18        21.04        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6A 
       22.09        18.41        32.94 

$`1Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 
        6.97         4.64         7.43        18.35        30.90         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-6706 
       19.33        39.12        26.10         9.17        32.78        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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       15.42        28.01        15.32        12.43         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       18.71        17.49        14.43        11.44         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05         0.56         2.66        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40        19.50        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-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 
       19.17        14.79        15.85         3.72        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
        9.86        15.68        10.68        12.56        13.87         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36         0.46        20.65 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.13         0.10         0.10         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        11.31        12.43        12.20         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
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-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
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        12.36 
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-D7-6528 TCGA-D7-6815 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       15.22        15.98        16.80        17.19        18.21        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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        13.71        11.24        11.44         9.76        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
        8.38         4.34         7.40         7.13        16.24        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27        11.38        19.53        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8602 
        5.03         0.23        18.08         1.51        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20         3.25        22.75        21.37        29.98 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51        10.19         0.26         2.10        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.30         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38         5.36         5.19        13.08 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
       13.51         2.53         5.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       19.73         9.86        45.67         8.52        61.25         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-A8NB TCGA-SW-A7EA 
       40.64       116.38        71.38        57.44        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.79         0.92        13.25        13.02        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO 
       16.31        22.19         2.50        12.79         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
       23.41        15.65        13.35        26.24        27.35        64.57 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       11.70        11.93        61.22        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       36.16         7.36         9.50         9.73        52.24         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P 
        2.01        55.43         4.54         6.58         5.72         2.66 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       40.08        28.41        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.07              0.00 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           115.69            122.30 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            12.79             13.02 
[1] "0.1 - 115.7 (12.8)" "0.0 - 122.3 (13.0)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         1        5       11        7         7        11
  1Q GAIN WILD-TYPE       2        9       30       24        31        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           2         21         17          9        7
  1Q GAIN WILD-TYPE         2         64         45         32       39
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 5                 9
  STAGE IB                11                30
  STAGE II                 7                24
  STAGE IIA                7                31
  STAGE IIB               11                44
  STAGE III                2                 2
  STAGE IIIA              21                64
  STAGE IIIB              17                45
  STAGE IIIC               9                32
  STAGE IV                 7                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
  1Q GAIN MUTATED     7  21  48  25
  1Q GAIN WILD-TYPE  15  69 147  94
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               7                15
  T2              21                69
  T3              48               147
  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
  1Q GAIN MUTATED   30 20 25 21
  1Q GAIN WILD-TYPE 99 98 59 68
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              30                99
  N1              20                98
  N2              25                59
  N3              21                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"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    91   5
  1Q GAIN WILD-TYPE 296  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     91    5
  1Q GAIN WILD-TYPE  296   25
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              91               296
  1               5                25
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    34  69
  1Q GAIN WILD-TYPE 124 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     34   69
  1Q GAIN WILD-TYPE  124  209
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              34               124
  MALE                69               209
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1Q GAIN MUTATED                                      12
  1Q GAIN WILD-TYPE                                    59
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                       37
  1Q GAIN WILD-TYPE                                                    125
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                                  20
  1Q GAIN WILD-TYPE                                                                61
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  1Q GAIN MUTATED                                                 26
  1Q GAIN WILD-TYPE                                               52
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  1Q GAIN MUTATED                                                          3
  1Q GAIN WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  1Q GAIN MUTATED                                                           1
  1Q GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  1Q GAIN MUTATED                                          4
  1Q GAIN WILD-TYPE                                        9
D2V8, multiclass
                                                                   clus
vv                                                                  1Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         37
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        4
                                                                   clus
vv                                                                  1Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          9
[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"
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     2 101
  1Q GAIN WILD-TYPE   4 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2  101
  1Q GAIN WILD-TYPE    4  329
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                2                 4
  YES             101               329
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    80   5   3   7
  1Q GAIN WILD-TYPE 267  13  16  18
D2V10, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              80               267
  R1               5                13
  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                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           0    66
  1Q GAIN WILD-TYPE                                         1   208
D2V12, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                                  23                65
  BLACK OR AFRICAN AMERICAN                               6                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  66               208
[1] 4 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   4 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   81
  1Q GAIN WILD-TYPE    4  232
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              81               232
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    46  25
  2P GAIN WILD-TYPE 208 125
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               71               333 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               25               125 
$`2P GAIN MUTATED`
TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6566 TCGA-BR-7197 TCGA-BR-7704 
       11.01         6.61        17.29        32.78         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 TCGA-BR-8362 
       15.42        18.15         0.69         9.60         2.20        13.08 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J8 
        5.39         9.21        20.22         1.48        12.89        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 
       20.65        20.42        13.15        13.18         0.30         0.07 
TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-6521 
       21.99        12.00        36.00        12.03        79.07        18.54 
TCGA-D7-6815 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-HU-8249 
       15.98        18.21        16.44        11.24        15.65        14.17 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP 
        0.76        24.30        12.30        22.75        25.81         8.98 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 
        2.10        12.95        23.84        12.30        27.42         3.45 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A93H 
        1.41         6.74        12.59         5.56         5.56        37.64 
TCGA-MX-A663 TCGA-R5-A7ZE TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PE TCGA-VQ-A8PH 
        9.86        18.21        35.24        21.73        22.19        12.79 
TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6A 
       17.85        20.81         1.71        64.18        40.08        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        16.14        21.11        10.62         0.79 

$`2P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       26.70        11.70        19.56         9.47         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       12.82        24.76        23.93        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44        12.26        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95         2.66        16.31        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 
        0.26        15.85         3.72        25.18         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI 
       12.82         0.66        19.36         0.46         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8525 
       11.57         5.13         2.83         3.25         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.13         0.13         0.10         3.42         9.34 
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         0.10 
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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98        30.97         6.97         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-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        12.79        10.55 
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-D7-8576 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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        2.96         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.99        16.24        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-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       12.10        10.62         5.59        11.84        24.20         3.25 
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         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       10.19         0.26        19.36         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21        18.81         3.39        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       13.08         6.44         6.51         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 
        2.53        60.56        20.15         3.72        19.73        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         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-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        18.48        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        28.96        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V 
       11.70        11.93        61.22        18.74        22.68        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        7.36         9.50         9.73        52.24         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D 
       42.54        11.24        22.09        18.41        28.41        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       54.12        26.04        12.43 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.00 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            79.07            122.30 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            13.51             12.62 
[1] "0.1 - 79.1 (13.5)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         0        5        6        7         7        11
  2P GAIN WILD-TYPE       3        9       35       24        31        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           1         13         10          9        6
  2P GAIN WILD-TYPE         3         72         52         32       40
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 5                 9
  STAGE IB                 6                35
  STAGE II                 7                24
  STAGE IIA                7                31
  STAGE IIB               11                44
  STAGE III                1                 3
  STAGE IIIA              13                72
  STAGE IIIB              10                52
  STAGE IIIC               9                32
  STAGE IV                 6                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
  2P GAIN MUTATED     5  12  39  19
  2P GAIN WILD-TYPE  17  78 156 100
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               5                17
  T2              12                78
  T3              39               156
  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  15  14  19
  2P GAIN WILD-TYPE 103 103  70  70
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              26               103
  N1              15               103
  N2              14                70
  N3              19                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"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    70   4
  2P GAIN WILD-TYPE 317  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     70    4
  2P GAIN WILD-TYPE  317   26
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              70               317
  1               4                26
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    28  48
  2P GAIN WILD-TYPE 130 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     28   48
  2P GAIN WILD-TYPE  130  230
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              28               130
  MALE                48               230
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  2P GAIN MUTATED                                       8
  2P GAIN WILD-TYPE                                    63
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                       26
  2P GAIN WILD-TYPE                                                    136
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                                  17
  2P GAIN WILD-TYPE                                                                64
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  2P GAIN MUTATED                                                 20
  2P GAIN WILD-TYPE                                               58
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  2P GAIN MUTATED                                                          1
  2P GAIN WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  2P GAIN MUTATED                                                           3
  2P GAIN WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  2P GAIN MUTATED                                          0
  2P GAIN WILD-TYPE                                       13
D3V8, multiclass
                                                                   clus
vv                                                                  2P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  2P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          136
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         13
[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"
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  76
  2P GAIN WILD-TYPE   6 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   76
  2P GAIN WILD-TYPE    6  354
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                0                 6
  YES              76               354
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    66   1   3   2
  2P GAIN WILD-TYPE 281  17  16  23
D3V10, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              66               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      21                         1
  2P GAIN WILD-TYPE    67                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           0    45
  2P GAIN WILD-TYPE                                         1   229
D3V12, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                                  21                67
  BLACK OR AFRICAN AMERICAN                               1                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  45               229
[1] 4 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  54
  2P GAIN WILD-TYPE   4 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   54
  2P GAIN WILD-TYPE    4  259
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              54               259
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    37  23
  2Q GAIN WILD-TYPE 217 127
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               60               344 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               23               127 
$`2Q GAIN MUTATED`
TCGA-B7-A5TJ TCGA-BR-6456 TCGA-BR-6566 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       11.01        17.29        32.78         9.21        35.24        15.42 
TCGA-BR-7717 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 TCGA-BR-8362 TCGA-BR-8483 
       18.15         0.69         9.60         2.20        13.08         5.39 
TCGA-BR-8485 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PE 
        9.21         1.48        12.89         0.66        13.51        20.42 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-A48C TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5718 
       13.18         0.07        11.61        21.99        12.00        36.00 
TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-A4YU TCGA-D7-A6EV 
       12.03        79.07        18.54        15.98        16.44        11.24 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF 
        7.99        72.23         0.76        24.30        12.30        25.81 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-A6RR 
        2.10        12.95        23.84        12.30         3.45         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-VQ-A8E2 
       12.59         5.56         5.56        37.64         9.86        35.24 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D 
       22.19        12.79        17.85        20.81         1.71        64.18 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       32.94        29.98        16.14        21.11        10.62         0.79 

$`2Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       32.94        12.82        24.76        23.93        28.01        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43        11.44        12.26        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        0.56        12.95         2.66        16.31        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 
       14.79         0.26        15.85         3.72        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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        6.08        22.26        13.41        13.51         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
       14.17         0.53        12.82        19.36         0.46        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        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         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        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        12.36        12.66        11.93        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        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
        8.38         4.34         7.40         7.13         0.62        16.24 
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-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        5.52         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
        5.59        11.84        24.20         3.25        22.75        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         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       10.19         0.26        19.36         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42        21.21        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU 
        5.19        13.08         1.41         6.44         6.51         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG 
        7.82        13.51         2.53        60.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        45.67        18.21         8.52        61.25         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-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-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
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-A8PU 
        9.27        23.41        15.65        13.35        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        18.74        22.68        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        52.24         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-A94T 
        6.58         5.72        21.04         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F 
       22.09        18.41        40.08        28.41        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6K 
       26.04        12.43 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.07              0.00 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            79.07            122.30 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           12.920            12.805 
[1] "0.1 - 79.1 (12.9)"  "0.0 - 122.3 (12.8)"
[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        11
  2Q GAIN WILD-TYPE       3       10       36       26        32        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           1          8         10          7        6
  2Q GAIN WILD-TYPE         3         77         52         34       40
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 4                10
  STAGE IB                 5                36
  STAGE II                 5                26
  STAGE IIA                6                32
  STAGE IIB               11                44
  STAGE III                1                 3
  STAGE IIIA               8                77
  STAGE IIIB              10                52
  STAGE IIIC               7                34
  STAGE IV                 6                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
  2Q GAIN MUTATED     3  11  34  16
  2Q GAIN WILD-TYPE  19  79 161 103
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               3                19
  T2              11                79
  T3              34               161
  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
  2Q GAIN MUTATED    21  14  10  17
  2Q GAIN WILD-TYPE 108 104  74  72
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              21               108
  N1              14               104
  N2              10                74
  N3              17                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"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    57   4
  2Q GAIN WILD-TYPE 330  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     57    4
  2Q GAIN WILD-TYPE  330   26
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              57               330
  1               4                26
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    24  41
  2Q GAIN WILD-TYPE 134 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     24   41
  2Q GAIN WILD-TYPE  134  237
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              24               134
  MALE                41               237
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  2Q GAIN MUTATED                                       6
  2Q GAIN WILD-TYPE                                    65
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                       25
  2Q GAIN WILD-TYPE                                                    137
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                                  17
  2Q GAIN WILD-TYPE                                                                64
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  2Q GAIN MUTATED                                                 13
  2Q GAIN WILD-TYPE                                               65
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  2Q GAIN MUTATED                                                          1
  2Q GAIN WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  2Q GAIN MUTATED                                                           2
  2Q GAIN WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  2Q GAIN MUTATED                                          0
  2Q GAIN WILD-TYPE                                       13
D4V8, multiclass
                                                                   clus
vv                                                                  2Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  2Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 65
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         13
[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"
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  65
  2Q GAIN WILD-TYPE   6 365
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   65
  2Q GAIN WILD-TYPE    6  365
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                0                 6
  YES              65               365
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    55   1   3   2
  2Q GAIN WILD-TYPE 292  17  16  23
D4V10, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              55               292
  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      15                         2
  2Q GAIN WILD-TYPE    73                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           0    40
  2Q GAIN WILD-TYPE                                         1   234
D4V12, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                                  15                73
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  40               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"
D4V13, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  46
  2Q GAIN WILD-TYPE   4 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   46
  2Q GAIN WILD-TYPE    4  267
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              46               267
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    32  16
  3P GAIN WILD-TYPE 222 134
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               48               356 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               16               134 
$`3P GAIN MUTATED`
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 
        6.18        34.68         9.17        30.90        12.82        15.32 
TCGA-BR-7901 TCGA-BR-8296 TCGA-BR-8373 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-CD-5799 
        3.45        15.58        14.79        19.36        20.65         3.25 
TCGA-CD-5801 TCGA-CD-8528 TCGA-CG-4444 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5727 
       13.18         0.10        47.05        30.97        12.03        79.07 
TCGA-D7-6815 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-F1-A448 TCGA-FP-7998 
       15.98        16.44        11.24         2.96        21.27        22.29 
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-A4H5 TCGA-HU-A4HD TCGA-R5-A7ZR TCGA-RD-A8N9 TCGA-VQ-A8DT 
       19.36        12.30        27.42         6.08        35.61        48.79 
TCGA-VQ-A8P5 TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        7.73        17.85        23.41        13.35        64.57        65.16 
TCGA-VQ-A91E TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A94O TCGA-VQ-AA6F 
       11.93         9.73         9.04         2.01        21.04        54.12 

$`3P GAIN WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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        21.11        31.20        32.94 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        28.73        12.43         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20         7.40         6.18        19.50        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-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        19.17         0.26        15.85         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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17         0.53        12.82         0.66        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        13.64        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        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         0.10        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-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         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-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        12.36        12.66        11.93 
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-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        12.79        10.55 
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-A4YV 
       18.21        14.66        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        0.62         7.99        16.24        14.47        72.23        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-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         0.56         5.52         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       11.84         3.25        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H6 
        6.51         6.25        10.19         0.26        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.38         5.36         5.19        13.08         1.41         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         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
       13.51         2.53         5.56        60.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73         9.86        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       61.25         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-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        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88        32.48        28.96        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-A8PU TCGA-VQ-A8PY 
        1.87         9.27        15.65        26.24        27.35        14.33 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       36.69        11.70        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A924 
        1.71        36.16         7.36         9.50        52.24        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58         5.72        64.18         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       11.24        22.09        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        17.13        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              0.1               0.0 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            79.07            122.30 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           15.780            12.605 
[1] "0.1 - 79.1 (15.8)"  "0.0 - 122.3 (12.6)"
[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         9
  3P GAIN WILD-TYPE       3       12       36       27        34        46
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           1          9          6          7        5
  3P GAIN WILD-TYPE         3         76         56         34       41
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 2                12
  STAGE IB                 5                36
  STAGE II                 4                27
  STAGE IIA                4                34
  STAGE IIB                9                46
  STAGE III                1                 3
  STAGE IIIA               9                76
  STAGE IIIB               6                56
  STAGE IIIC               7                34
  STAGE IV                 5                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
  3P GAIN MUTATED     2  11  23  16
  3P GAIN WILD-TYPE  20  79 172 103
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               2                20
  T2              11                79
  T3              23               172
  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  14   7  13
  3P GAIN WILD-TYPE 113 104  77  76
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              16               113
  N1              14               104
  N2               7                77
  N3              13                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"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    50   2
  3P GAIN WILD-TYPE 337  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     50    2
  3P GAIN WILD-TYPE  337   28
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              50               337
  1               2                28
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    21  32
  3P GAIN WILD-TYPE 137 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     21   32
  3P GAIN WILD-TYPE  137  246
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              21               137
  MALE                32               246
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3P GAIN MUTATED                                       8
  3P GAIN WILD-TYPE                                    63
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                       15
  3P GAIN WILD-TYPE                                                    147
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                                  13
  3P GAIN WILD-TYPE                                                                68
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  3P GAIN MUTATED                                                 13
  3P GAIN WILD-TYPE                                               65
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3P GAIN MUTATED                                                          2
  3P GAIN WILD-TYPE                                                       19
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  3P GAIN MUTATED                                                           1
  3P GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3P GAIN MUTATED                                          1
  3P GAIN WILD-TYPE                                       12
D5V8, multiclass
                                                                   clus
vv                                                                  3P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  3P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          147
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 65
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         12
[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"
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  53
  3P GAIN WILD-TYPE   6 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   53
  3P GAIN WILD-TYPE    6  377
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                 6
  YES              53               377
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    44   1   2   4
  3P GAIN WILD-TYPE 303  17  17  21
D5V10, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              44               303
  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"
D5V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED      14                         2
  3P GAIN WILD-TYPE    74                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           0    28
  3P GAIN WILD-TYPE                                         1   246
D5V12, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                                  14                74
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  28               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"
D5V13, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  33
  3P GAIN WILD-TYPE   2 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   33
  3P GAIN WILD-TYPE    2  280
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              33               280
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    55  31
  3Q GAIN WILD-TYPE 199 119
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               86               318 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               31               119 
$`3Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-6802 TCGA-BR-7196 
       11.70         6.18        34.68         9.17        30.90        12.82 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 
       15.32        28.73         3.45         8.05         2.20        15.58 
TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 
       19.50        26.33        14.79        25.18        12.79        15.81 
TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-5801 
        0.53        19.36        20.65        20.42         3.25        13.18 
TCGA-CD-5803 TCGA-CD-8527 TCGA-CD-8528 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4444 
        0.07         0.07         0.10        15.95         7.99        47.05 
TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-6521 
       12.03        12.00        30.97        12.03        79.07        18.54 
TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-F1-A448 
       15.98        24.72        16.44        11.24         2.96        21.27 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
       14.07        22.29        26.47        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
       22.75        25.81         8.98         2.10        12.95        19.36 
TCGA-HU-A4HD TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F7 TCGA-R5-A7ZR 
       27.42         6.44         5.56         1.81        60.56         6.08 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       37.91       115.69        35.61        48.79        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP 
       35.24        21.73         7.73         2.70        17.85        23.41 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Y 
       13.35        27.35        64.57        65.16        11.93         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        32.94        54.12 
TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       21.11         0.79 

$`3Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        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-4279 
        6.97         4.64         7.43        18.35        30.90         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        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-6803 TCGA-BR-6852 TCGA-BR-7197 
       12.16         8.98        21.11        31.20        32.94         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01        18.15 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       11.44         0.69        12.26         9.60        20.55         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
       12.95         2.66        16.31         7.40         6.18        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19        17.52         0.95         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        19.17         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8591 
        5.39         9.21        20.22         1.12         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
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        12.82         0.66 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        2.83        13.15         0.30         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        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         0.10        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-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98         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-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.31        11.44         9.76 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        7.99        16.24        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       19.53        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        5.52         0.23        18.08         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.30         5.59        11.84        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H4 
        0.10         6.51         6.25        10.19         0.26        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88         8.81        21.21         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         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
        1.41         6.74        12.59         6.51         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
        9.86        45.67        18.21         8.52        61.25         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        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88        32.48        28.96        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 
       26.24        14.33        36.69        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        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       52.24        55.43         6.58         5.72        64.18         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.54        11.24        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       29.98        17.13        26.04        16.14        12.43        10.62 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.07              0.00 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           115.69            122.30 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           15.695            12.495 
[1] "0.1 - 115.7 (15.7)" "0.0 - 122.3 (12.5)"
[1] "hr=" "1.3"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         0        3       10        8         5        11
  3Q GAIN WILD-TYPE       3       11       31       23        33        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           1         15         16         14        8
  3Q GAIN WILD-TYPE         3         70         46         27       38
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 3                11
  STAGE IB                10                31
  STAGE II                 8                23
  STAGE IIA                5                33
  STAGE IIB               11                44
  STAGE III                1                 3
  STAGE IIIA              15                70
  STAGE IIIB              16                46
  STAGE IIIC              14                27
  STAGE IV                 8                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
  3Q GAIN MUTATED     5  19  36  32
  3Q GAIN WILD-TYPE  17  71 159  87
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               5                17
  T2              19                71
  T3              36               159
  T4              32                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"
                   vv
clus                 N0  N1  N2  N3
  3Q GAIN MUTATED    25  23  18  23
  3Q GAIN WILD-TYPE 104  95  66  66
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              25               104
  N1              23                95
  N2              18                66
  N3              23                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"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    83   4
  3Q GAIN WILD-TYPE 304  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     83    4
  3Q GAIN WILD-TYPE  304   26
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              83               304
  1               4                26
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    34  59
  3Q GAIN WILD-TYPE 124 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     34   59
  3Q GAIN WILD-TYPE  124  219
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              34               124
  MALE                59               219
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3Q GAIN MUTATED                                      13
  3Q GAIN WILD-TYPE                                    58
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                       31
  3Q GAIN WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                                  22
  3Q GAIN WILD-TYPE                                                                59
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  3Q GAIN MUTATED                                                 19
  3Q GAIN WILD-TYPE                                               59
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3Q GAIN MUTATED                                                          3
  3Q GAIN WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  3Q GAIN MUTATED                                                           1
  3Q GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3Q GAIN MUTATED                                          3
  3Q GAIN WILD-TYPE                                       10
D6V8, multiclass
                                                                   clus
vv                                                                  3Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  3Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         10
[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"
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     1  92
  3Q GAIN WILD-TYPE   5 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   92
  3Q GAIN WILD-TYPE    5  338
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                1                 5
  YES              92               338
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    77   2   5   5
  3Q GAIN WILD-TYPE 270  16  14  20
D6V10, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              77               270
  R1               2                16
  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"
D6V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED      20                         5
  3Q GAIN WILD-TYPE    68                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           0    52
  3Q GAIN WILD-TYPE                                         1   222
D6V12, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                                  20                68
  BLACK OR AFRICAN AMERICAN                               5                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  52               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"
D6V13, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     2  58
  3Q GAIN WILD-TYPE   2 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   58
  3Q GAIN WILD-TYPE    2  255
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              58               255
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    13   8
  4P GAIN WILD-TYPE 241 142
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               21               383 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               142 
$`4P GAIN MUTATED`
TCGA-BR-8484 TCGA-BR-A4IY TCGA-CD-8528 TCGA-CG-4443 TCGA-CG-4475 TCGA-CG-5720 
       25.18        12.89         0.10        29.98        22.98         0.99 
TCGA-CG-5722 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-HU-A4GH 
        0.99        12.66        11.93        11.24        15.65        11.77 
TCGA-IN-7806 TCGA-IN-A7NT TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU 
       21.21         5.56        17.85         1.87        13.35        27.35 
TCGA-VQ-A91Q TCGA-VQ-A92D TCGA-VQ-AA6K 
       20.81        64.18        12.43 

$`4P GAIN WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       18.71        17.49        14.43        11.44         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        22.26         1.48        13.41        13.51         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        12.82         0.66        19.36 
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        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        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         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        47.05        19.07        12.03        21.99 
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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        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        12.36        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-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        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-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        2.96         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.99        16.24        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-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        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         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       12.30         9.67         8.88         8.81        27.42         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         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
        1.41         6.44         6.74        12.59         6.51         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         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-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        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-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        26.24        64.57        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       36.69        11.70        11.93        61.22        18.74        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        36.16         7.36         9.50         9.73        52.24 
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-A94U TCGA-VQ-AA64 
       21.04         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       40.08        28.41        32.94        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        21.11        10.62         0.79 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
              0.1               0.0 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            64.18            122.30 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            12.89             12.82 
[1] "0.1 - 64.2 (12.9)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         0        2        3        0         0         4
  4P GAIN WILD-TYPE       3       12       38       31        38        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           0          7          1          1        3
  4P GAIN WILD-TYPE         4         78         61         40       43
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 2                12
  STAGE IB                 3                38
  STAGE II                 0                31
  STAGE IIA                0                38
  STAGE IIB                4                51
  STAGE III                0                 4
  STAGE IIIA               7                78
  STAGE IIIB               1                61
  STAGE IIIC               1                40
  STAGE IV                 3                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
  4P GAIN MUTATED     2   4   9   6
  4P GAIN WILD-TYPE  20  86 186 113
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               2                20
  T2               4                86
  T3               9               186
  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     7   6   4   4
  4P GAIN WILD-TYPE 122 112  80  85
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               7               122
  N1               6               112
  N2               4                80
  N3               4                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 367  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     20    1
  4P GAIN WILD-TYPE  367   29
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              20               367
  1               1                29
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     5  16
  4P GAIN WILD-TYPE 153 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5   16
  4P GAIN WILD-TYPE  153  262
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               5               153
  MALE                16               262
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  4P GAIN MUTATED                                       1
  4P GAIN WILD-TYPE                                    70
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                        6
  4P GAIN WILD-TYPE                                                    156
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                                   4
  4P GAIN WILD-TYPE                                                                77
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  4P GAIN MUTATED                                                  6
  4P GAIN WILD-TYPE                                               72
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  4P GAIN MUTATED                                                          1
  4P GAIN WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  4P GAIN MUTATED                                                           0
  4P GAIN WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  4P GAIN MUTATED                                          2
  4P GAIN WILD-TYPE                                       11
D7V8, multiclass
                                                                   clus
vv                                                                  4P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  4P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            70
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                77
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 72
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         11
[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"
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  21
  4P GAIN WILD-TYPE   6 409
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   21
  4P GAIN WILD-TYPE    6  409
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                0                 6
  YES              21               409
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    18   2   1   0
  4P GAIN WILD-TYPE 329  16  18  25
D7V10, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              18               329
  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       3                         0
  4P GAIN WILD-TYPE    85                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0    13
  4P GAIN WILD-TYPE                                         1   261
D7V12, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                                   3                85
  BLACK OR AFRICAN AMERICAN                               0                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               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"
D7V13, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  10
  4P GAIN WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   10
  4P GAIN WILD-TYPE    4  303
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               303
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     7   9
  4Q GAIN WILD-TYPE 247 141
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               388 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               141 
$`4Q GAIN MUTATED`
TCGA-BR-8484 TCGA-CG-4475 TCGA-CG-5720 TCGA-CG-5722 TCGA-D7-5578 TCGA-D7-A6EV 
       25.18        22.98         0.99         0.99        12.66        11.24 
TCGA-HJ-7597 TCGA-HU-8249 TCGA-IN-7806 TCGA-RD-A8N5 TCGA-VQ-A8PK TCGA-VQ-A8PM 
       26.47        14.17        21.21        57.44        17.85         1.87 
TCGA-VQ-A8PU TCGA-VQ-A91Q TCGA-VQ-A92D TCGA-VQ-A94T 
       27.35        20.81        64.18        11.24 

$`4Q GAIN WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       18.71        17.49        14.43        11.44         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        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        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        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 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.13         0.13         0.10         3.42         9.34        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         0.10        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-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         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-5727 
        6.02       105.07        12.03        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        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-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34         7.40         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        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-A8CX TCGA-HF-A5NB TCGA-HU-8238 
       13.58         0.56         5.52         0.23        18.08         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        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         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        27.42         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.38         5.36         5.19        13.08         1.41         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         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
       13.51         2.53         5.56        60.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73         9.86        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         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-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-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        28.96        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        26.24        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        11.93        61.22        18.74        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       36.16         7.36         9.50         9.73        52.24         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-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       32.94        29.98        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.99              0.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            64.18            122.30 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            19.33             12.79 
[1] "1.0 - 64.2 (19.3)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         0        0        3        0         0         3
  4Q GAIN WILD-TYPE       3       14       38       31        38        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           0          5          2          0        3
  4Q GAIN WILD-TYPE         4         80         60         41       43
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 0                14
  STAGE IB                 3                38
  STAGE II                 0                31
  STAGE IIA                0                38
  STAGE IIB                3                52
  STAGE III                0                 4
  STAGE IIIA               5                80
  STAGE IIIB               2                60
  STAGE IIIC               0                41
  STAGE IV                 3                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
  4Q GAIN MUTATED     0   4   9   3
  4Q GAIN WILD-TYPE  22  86 186 116
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                22
  T2               4                86
  T3               9               186
  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     3   5   5   3
  4Q GAIN WILD-TYPE 126 113  79  86
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               3               126
  N1               5               113
  N2               5                79
  N3               3                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 373  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     14    1
  4Q GAIN WILD-TYPE  373   29
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              14               373
  1               1                29
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4  12
  4Q GAIN WILD-TYPE 154 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4   12
  4Q GAIN WILD-TYPE  154  266
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4               154
  MALE                12               266
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  4Q GAIN MUTATED                                       2
  4Q GAIN WILD-TYPE                                    69
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                        3
  4Q GAIN WILD-TYPE                                                    159
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                                   2
  4Q GAIN WILD-TYPE                                                                79
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  4Q GAIN MUTATED                                                  5
  4Q GAIN WILD-TYPE                                               73
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  4Q GAIN MUTATED                                                          1
  4Q GAIN WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  4Q GAIN MUTATED                                                           0
  4Q GAIN WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  4Q GAIN MUTATED                                          2
  4Q GAIN WILD-TYPE                                       11
D8V8, multiclass
                                                                   clus
vv                                                                  4Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  4Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            69
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          159
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                79
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 73
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         11
[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"
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0  16
  4Q GAIN WILD-TYPE   6 414
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   16
  4Q GAIN WILD-TYPE    6  414
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                 6
  YES              16               414
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    15   0   1   0
  4Q GAIN WILD-TYPE 332  18  18  25
D8V10, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              15               332
  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       1                         0
  4Q GAIN WILD-TYPE    87                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0    10
  4Q GAIN WILD-TYPE                                         1   264
D8V12, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                                   1                87
  BLACK OR AFRICAN AMERICAN                               0                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               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"
D8V13, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   7
  4Q GAIN WILD-TYPE   4 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    7
  4Q GAIN WILD-TYPE    4  306
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               306
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    58  35
  5P GAIN WILD-TYPE 196 115
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               93               311 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               35               115 
$`5P GAIN MUTATED`
TCGA-BR-4187 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 
        4.64        35.24        15.42        28.01        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        12.95         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 
       11.54         8.22        20.65        13.18         0.07         0.07 
TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 
        0.10         3.42        11.61         7.99        54.08        14.01 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       47.05        12.03        21.99        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       22.98        36.00         0.99        12.03        15.02         4.01 
TCGA-D7-5579 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       11.93        10.26        15.22        10.55        11.31        24.72 
TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 
       14.66        11.31         2.96        15.65         0.62         7.99 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 
       19.53        17.06         0.23         1.51        12.59        14.17 
TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H0 TCGA-HU-A4H5 
       24.30         3.25        22.75        25.81         2.10        12.30 
TCGA-HU-A4HD TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93G 
       27.42         6.51         5.56         1.81         5.56        20.15 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU 
       45.67        18.21        57.44         8.94        35.61         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PK TCGA-VQ-A91A 
       13.25        18.48        35.24        21.73        17.85        36.69 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F 
        9.50        52.24        11.24        40.08        32.94        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       16.14        21.11        12.43 

$`5P GAIN WILD-TYPE`
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-4267 
        6.61         6.97         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       23.93        15.32        28.73        12.43         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43        12.26         9.60        20.55 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.56        16.31         2.20         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       13.08        22.19         0.95         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        19.17         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        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        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.13         0.10         9.34        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         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 
       27.02        15.95         1.02         8.05         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       19.07         0.00         9.01        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99         6.02       105.07        28.96        79.07        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       69.04        21.07         7.99        12.36        12.66        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-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       17.19        15.98        12.79        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        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         8.38         4.34         7.40         7.13 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        14.47        72.23        21.27        11.38         3.48 
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-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
        5.52        18.08        26.47         5.92        14.27        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10        10.62         0.76         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       24.20        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.25        10.19         0.26        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.84         9.67         8.88         8.81        21.21         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         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1V TCGA-IN-AB1X 
        1.41         6.44         6.74        12.59         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53        60.56        37.64         3.72        19.73         9.86 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         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        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        28.96        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       65.16        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 
       22.68         1.71        36.16         7.36         9.73         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        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 
       21.04         2.66        42.54        22.09        18.41        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        17.13        26.04        10.62         0.79 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.07              0.00 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            57.44            122.30 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            13.18             12.79 
[1] "0.1 - 57.4 (13.2)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         0        1       11        8         8        12
  5P GAIN WILD-TYPE       3       13       30       23        30        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED           0         20         12         11       12
  5P GAIN WILD-TYPE         4         65         50         30       34
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 1                13
  STAGE IB                11                30
  STAGE II                 8                23
  STAGE IIA                8                30
  STAGE IIB               12                43
  STAGE III                0                 4
  STAGE IIIA              20                65
  STAGE IIIB              12                50
  STAGE IIIC              11                30
  STAGE IV                12                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
  5P GAIN MUTATED     1  24  50  22
  5P GAIN WILD-TYPE  21  66 145  97
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                21
  T2              24                66
  T3              50               145
  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
  5P GAIN MUTATED    25  28  22  21
  5P GAIN WILD-TYPE 104  90  62  68
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              25               104
  N1              28                90
  N2              22                62
  N3              21                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"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    88   8
  5P GAIN WILD-TYPE 299  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     88    8
  5P GAIN WILD-TYPE  299   22
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              88               299
  1               8                22
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    37  63
  5P GAIN WILD-TYPE 121 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     37   63
  5P GAIN WILD-TYPE  121  215
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              37               121
  MALE                63               215
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5P GAIN MUTATED                                       8
  5P GAIN WILD-TYPE                                    63
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                       31
  5P GAIN WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                                  29
  5P GAIN WILD-TYPE                                                                52
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  5P GAIN MUTATED                                                 17
  5P GAIN WILD-TYPE                                               61
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5P GAIN MUTATED                                                          7
  5P GAIN WILD-TYPE                                                       14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  5P GAIN MUTATED                                                           3
  5P GAIN WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5P GAIN MUTATED                                          3
  5P GAIN WILD-TYPE                                       10
D9V8, multiclass
                                                                   clus
vv                                                                  5P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  5P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         10
[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"
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     2  98
  5P GAIN WILD-TYPE   4 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   98
  5P GAIN WILD-TYPE    4  332
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                2                 4
  YES              98               332
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    81   4   5   5
  5P GAIN WILD-TYPE 266  14  14  20
D9V10, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              81               266
  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      18                         2
  5P GAIN WILD-TYPE    70                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           0    62
  5P GAIN WILD-TYPE                                         1   212
D9V12, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                                  18                70
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  62               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"
D9V13, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1  65
  5P GAIN WILD-TYPE   3 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   65
  5P GAIN WILD-TYPE    3  248
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              65               248
[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 228 136
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               40               364 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               14               136 
$`5Q GAIN MUTATED`
TCGA-BR-7715 TCGA-BR-8284 TCGA-BR-8296 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-A4PD 
       15.42         8.05        15.58        17.52        26.33        20.65 
TCGA-CD-8524 TCGA-CD-A486 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4455 TCGA-CG-4466 
        0.07         3.42         7.99        54.08        12.03        18.97 
TCGA-CG-4472 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-8576 
       12.00        15.02         4.01        15.22        24.72        14.66 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8099 TCGA-HU-8238 
       15.65         0.62         7.99        19.53        17.06         1.51 
TCGA-HU-8249 TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       14.17         2.10        12.30         6.51         5.56         1.81 
TCGA-KB-A6F5 TCGA-KB-A93G TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-VQ-A8E0 TCGA-VQ-A91X 
        5.56        20.15        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-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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        35.24        23.93        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         0.56        12.95         2.66        16.31         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50        13.08         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        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-A4PE 
       12.82         0.66        19.36        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.13         0.10         9.34        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         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 
        3.02        27.02        15.95         1.02         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        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 
       12.36        12.66        11.93        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-D7-6822 TCGA-D7-8572 
       15.98        12.79        10.55        11.31        12.33        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        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       11.24        11.31        11.44         9.76         2.96         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.40         7.13        16.24        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-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        14.27        12.59        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
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-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26        12.95        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.81        27.42        21.21         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.38         5.36         5.19        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
        6.74        12.59         7.82        13.51         2.53        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         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-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      115.69       116.38        71.38         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y 
       20.81        22.68         1.71        36.16         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       52.24         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-A94U 
        5.72        64.18        21.04         2.66        42.54        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        40.08        28.41        32.94        29.98        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        21.11        10.62         0.79 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.07              0.00 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            57.44            122.30 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           14.415            12.805 
[1] "0.1 - 57.4 (14.4)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         0        0        7        4         5         4
  5Q GAIN WILD-TYPE       3       14       34       27        33        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           0          6          6          5        5
  5Q GAIN WILD-TYPE         4         79         56         36       41
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 0                14
  STAGE IB                 7                34
  STAGE II                 4                27
  STAGE IIA                5                33
  STAGE IIB                4                51
  STAGE III                0                 4
  STAGE IIIA               6                79
  STAGE IIIB               6                56
  STAGE IIIC               5                36
  STAGE IV                 5                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
  5Q GAIN MUTATED     0  12  23   8
  5Q GAIN WILD-TYPE  22  78 172 111
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                22
  T2              12                78
  T3              23               172
  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    14  10   8  10
  5Q GAIN WILD-TYPE 115 108  76  79
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              14               115
  N1              10               108
  N2               8                76
  N3              10                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 349  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     38    3
  5Q GAIN WILD-TYPE  349   27
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              38               349
  1               3                27
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    14  29
  5Q GAIN WILD-TYPE 144 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     14   29
  5Q GAIN WILD-TYPE  144  249
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              14               144
  MALE                29               249
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5Q GAIN MUTATED                                       3
  5Q GAIN WILD-TYPE                                    68
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                       12
  5Q GAIN WILD-TYPE                                                    150
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                                  13
  5Q GAIN WILD-TYPE                                                                68
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  5Q GAIN MUTATED                                                  7
  5Q GAIN WILD-TYPE                                               71
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5Q GAIN MUTATED                                                          4
  5Q GAIN WILD-TYPE                                                       17
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  5Q GAIN MUTATED                                                           1
  5Q GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5Q GAIN MUTATED                                          2
  5Q GAIN WILD-TYPE                                       11
D10V8, multiclass
                                                                   clus
vv                                                                  5Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  5Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 71
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         11
[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"
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  42
  5Q GAIN WILD-TYPE   5 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   42
  5Q GAIN WILD-TYPE    5  388
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                1                 5
  YES              42               388
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    37   1   2   1
  5Q GAIN WILD-TYPE 310  17  17  24
D10V10, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              37               310
  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       7                         1
  5Q GAIN WILD-TYPE    81                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    25
  5Q GAIN WILD-TYPE                                         1   249
D10V12, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                                   7                81
  BLACK OR AFRICAN AMERICAN                               1                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  25               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"
D10V13, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  27
  5Q GAIN WILD-TYPE   4 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   27
  5Q GAIN WILD-TYPE    4  286
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              27               286
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    36  31
  6P GAIN WILD-TYPE 218 119
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               67               337 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               31               119 
$`6P GAIN MUTATED`
TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 
       11.01         6.61         6.97         9.17         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 
       15.42        18.15        11.44        12.95         2.66        14.04 
TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8686 
       14.79        25.18         9.21        20.22        11.54        15.68 
TCGA-BR-8690 TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C 
       10.68        20.42         3.25         3.42         9.34        11.61 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4477 
        7.99        54.08        12.03        21.99        18.97        30.97 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        10.26        15.22        10.55        11.31        12.33 
TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-8631 
       14.66        14.27         2.96         7.99         3.48         0.56 
TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-8663 
        5.52        14.17        25.81        23.84         9.67         3.39 
TCGA-IN-A6RI TCGA-IN-A6RO TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-RD-A8MW 
       18.38         1.41        45.67        18.21         8.61        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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 
       26.70        11.70        19.56         9.47         9.44         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       12.82        24.76        23.93        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.56        16.31         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 
       19.50        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        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       15.85         3.72         5.39         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       16.44         9.86         8.22        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        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        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51         0.46        20.65         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       11.57         5.13         2.83        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.10        11.31        12.43         6.58        12.20         0.10 
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-4444 TCGA-CG-4449 
        8.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        22.98         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-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        79.07        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        12.36        12.66        11.93 
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-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       13.35        15.98        12.79        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       17.19        18.21        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62        16.24        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.03        13.58         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        19.36        12.30         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       21.21         3.45        18.81         5.36         5.19        13.08 
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         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64         3.72        19.73         9.86         8.52        61.25 
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-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-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        16.31         2.50        12.79 
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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        61.22        20.81        22.68        36.16         7.36 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       52.24         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-A94U 
        5.72        64.18         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        40.08        28.41        32.94        29.98        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        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.56              0.00 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           115.69            122.30 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            12.33             12.82 
[1] "0.6 - 115.7 (12.3)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.4"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         1        2       11        6         4         9
  6P GAIN WILD-TYPE       2       12       30       25        34        46
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           0         17          9          4       10
  6P GAIN WILD-TYPE         4         68         53         37       36
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 2                12
  STAGE IB                11                30
  STAGE II                 6                25
  STAGE IIA                4                34
  STAGE IIB                9                46
  STAGE III                0                 4
  STAGE IIIA              17                68
  STAGE IIIB               9                53
  STAGE IIIC               4                37
  STAGE IV                10                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
  6P GAIN MUTATED     3  21  32  17
  6P GAIN WILD-TYPE  19  69 163 102
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               3                19
  T2              21                69
  T3              32               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    22  20  17  15
  6P GAIN WILD-TYPE 107  98  67  74
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              22               107
  N1              20                98
  N2              17                67
  N3              15                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"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    66   5
  6P GAIN WILD-TYPE 321  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     66    5
  6P GAIN WILD-TYPE  321   25
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              66               321
  1               5                25
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    29  47
  6P GAIN WILD-TYPE 129 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     29   47
  6P GAIN WILD-TYPE  129  231
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              29               129
  MALE                47               231
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6P GAIN MUTATED                                       3
  6P GAIN WILD-TYPE                                    68
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                       30
  6P GAIN WILD-TYPE                                                    132
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                                  22
  6P GAIN WILD-TYPE                                                                59
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  6P GAIN MUTATED                                                 17
  6P GAIN WILD-TYPE                                               61
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6P GAIN MUTATED                                                          1
  6P GAIN WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  6P GAIN MUTATED                                                           1
  6P GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6P GAIN MUTATED                                          2
  6P GAIN WILD-TYPE                                       11
D11V8, multiclass
                                                                   clus
vv                                                                  6P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  6P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         11
[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"
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     3  73
  6P GAIN WILD-TYPE   3 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3   73
  6P GAIN WILD-TYPE    3  357
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                3                 3
  YES              73               357
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    54   3   5   7
  6P GAIN WILD-TYPE 293  15  14  18
D11V10, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              54               293
  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                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           1    50
  6P GAIN WILD-TYPE                                         0   224
D11V12, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               4                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  50               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"
D11V13, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     1  56
  6P GAIN WILD-TYPE   3 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   56
  6P GAIN WILD-TYPE    3  257
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              56               257
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    28  27
  6Q GAIN WILD-TYPE 226 123
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               55               349 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               27               123 
$`6Q GAIN MUTATED`
TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       11.01         6.61         6.97         9.21        35.24        15.42 
TCGA-BR-7717 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 
       18.15        11.44        12.95         2.66        14.04        14.79 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 
       25.18         9.21        20.22        11.54        15.68        10.68 
TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CD-A486 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4460 
        0.72         3.25         3.42         7.99        54.08        21.99 
TCGA-CG-4466 TCGA-CG-4477 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 
       18.97        30.97        10.26        15.22        10.55        11.31 
TCGA-D7-6822 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-A4BF TCGA-HU-A4GT 
       12.33        14.27         7.99         3.48         5.52         6.51 
TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-R5-A7O7 
        9.67         3.45         3.39        18.38         1.41        45.67 
TCGA-RD-A7BT TCGA-RD-A8N6 TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PE 
        8.61         8.94        13.25        13.02        18.48        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X 
        2.70        17.85        18.74        22.68         1.71         9.50 
TCGA-VQ-A94R 
       42.54 

$`6Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 
       26.70        11.70        19.56         9.47         9.44         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       32.94        12.82        24.76        23.93        28.01        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        16.31         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        19.50        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        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8588 
        0.26        15.85         3.72         5.39         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44         9.86         8.22        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
       13.64        11.57         5.13         2.83        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         9.34        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         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        22.98         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        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        12.36        12.66        11.93        19.13        20.55 
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-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       15.98        12.79        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         0.62        16.24        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-8631 TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        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-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       12.30         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19        13.08         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         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        9.86        18.21         8.52        61.25         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-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-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        16.31         2.50        12.79 
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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y 
       11.93        61.22        20.81        36.16         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       52.24         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U 
        5.72        64.18        21.04         2.66        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        40.08        28.41        32.94        29.98        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        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.72              0.00 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            54.08            122.30 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            11.44             12.95 
[1] "0.7 - 54.1 (11.4)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.6"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         1        2        9        5         3         5
  6Q GAIN WILD-TYPE       2       12       32       26        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           1         14          7          2       11
  6Q GAIN WILD-TYPE         3         71         55         39       35
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 2                12
  STAGE IB                 9                32
  STAGE II                 5                26
  STAGE IIA                3                35
  STAGE IIB                5                50
  STAGE III                1                 3
  STAGE IIIA              14                71
  STAGE IIIB               7                55
  STAGE IIIC               2                39
  STAGE IV                11                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
  6Q GAIN MUTATED     3  17  23  17
  6Q GAIN WILD-TYPE  19  73 172 102
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               3                19
  T2              17                73
  T3              23               172
  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    18  18  11  13
  6Q GAIN WILD-TYPE 111 100  73  76
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              18               111
  N1              18               100
  N2              11                73
  N3              13                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"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    52   6
  6Q GAIN WILD-TYPE 335  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     52    6
  6Q GAIN WILD-TYPE  335   24
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              52               335
  1               6                24
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    23  39
  6Q GAIN WILD-TYPE 135 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     23   39
  6Q GAIN WILD-TYPE  135  239
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              23               135
  MALE                39               239
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6Q GAIN MUTATED                                       2
  6Q GAIN WILD-TYPE                                    69
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                       26
  6Q GAIN WILD-TYPE                                                    136
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                                  19
  6Q GAIN WILD-TYPE                                                                62
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  6Q GAIN MUTATED                                                 12
  6Q GAIN WILD-TYPE                                               66
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6Q GAIN MUTATED                                                          0
  6Q GAIN WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  6Q GAIN MUTATED                                                           1
  6Q GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6Q GAIN MUTATED                                          2
  6Q GAIN WILD-TYPE                                       11
D12V8, multiclass
                                                                   clus
vv                                                                  6Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  6Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            69
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          136
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 66
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         11
[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"
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3  59
  6Q GAIN WILD-TYPE   3 371
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   59
  6Q GAIN WILD-TYPE    3  371
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                3                 3
  YES              59               371
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    44   2   4   6
  6Q GAIN WILD-TYPE 303  16  15  19
D12V10, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              44               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                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           1    40
  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                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  40               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     1  43
  6Q GAIN WILD-TYPE   3 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   43
  6Q GAIN WILD-TYPE    3  270
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              43               270
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   109  70
  7P GAIN WILD-TYPE 145  80
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              179               225 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               70                80 
$`7P GAIN MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-6456 TCGA-BR-6565 
       11.70        11.01         6.97         4.64        17.29         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
       32.78        25.61        18.05        21.11         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       15.42        18.15         3.45        12.76        18.71        14.43 
TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 
        0.69         8.05         0.56        12.95         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 
        7.40        13.08         0.95         3.32        14.79         0.26 
TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        5.39        20.22         1.12        16.44         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J7 
       10.68        22.26         1.48         0.72         0.53        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
       13.51        20.65        20.42         1.15        13.64         3.25 
TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
       13.18         0.10         0.16         0.13         0.10         3.42 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 
       12.43        11.61         6.58        12.20        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4460 TCGA-CG-4469 
       15.95         7.99         4.01        14.01        21.99         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
       12.00        22.98        36.00        12.03        28.96        79.07 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        12.66        11.93        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       18.54        17.19        10.26        15.22        15.98        10.55 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6874 
       20.91        16.44        15.16         2.96        15.65        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC 
        0.23        26.47        14.17        24.30        12.30         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 
       22.75        25.81         8.98         0.10        10.19         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         9.67        27.42 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO 
        3.45        18.81         3.39        18.38         5.19         1.41 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        6.44        12.59         6.51         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64         9.86        45.67        18.21         8.52        61.25 
TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DT 
        6.08         8.61       122.30        57.44         8.94        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       13.25        35.24        21.73        34.45        34.29        46.26 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
        2.50        12.79        17.85        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       11.70        11.93        18.74        20.81         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
        7.36         9.50         2.01         4.54        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       11.24        22.09        40.08        32.94        29.98        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

$`7P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4188 
       26.70        19.56         9.47         9.44         6.61         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         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        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       12.82        24.76        23.93        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       12.43         9.07        17.49        11.44        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       20.55         2.66        16.31         6.18        19.50         0.26 
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-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 
       19.17        15.85         3.72        25.18         9.21        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       11.54        15.81        15.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       12.82         0.66         0.46        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A487 
        0.07         0.13         0.10         0.10         0.13         9.34 
TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 
       11.31         0.10        12.62         3.02         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       54.08        29.98        47.05        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-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       69.04        12.36        20.55        18.61        17.85        13.35 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A4YV 
       12.79        11.31        16.80        19.50        14.27         5.92 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        9.76         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-8209 TCGA-FP-8210 
        7.99        16.24        21.27        11.38        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       13.58         0.56         5.52        18.08         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       14.27        12.59        11.41        12.10        10.62         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        5.59        11.84        24.20        11.77        21.37        29.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        6.51         6.25         0.26         8.88         8.81        21.21 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        5.36        13.08         6.74         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-R5-A805 
       13.51         2.53         3.72        19.73         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-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        0.92         5.46        13.02        18.48        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PM 
        7.73        28.96        16.31        22.19         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU 
        9.27        23.41        15.65        13.35        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       64.57        61.22        22.68         9.73        52.24         9.04 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 
       55.43         6.58         5.72        64.18         2.66        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
       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 
            13.64             12.43 
[1] "0.1 - 122.3 (13.6)" "0.0 - 116.4 (12.4)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         3        6       19       14        16        23
  7P GAIN WILD-TYPE       0        8       22       17        22        32
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           3         38         28         22       17
  7P GAIN WILD-TYPE         1         47         34         19       29
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  3                 0
  STAGE IA                 6                 8
  STAGE IB                19                22
  STAGE II                14                17
  STAGE IIA               16                22
  STAGE IIB               23                32
  STAGE III                3                 1
  STAGE IIIA              38                47
  STAGE IIIB              28                34
  STAGE IIIC              22                19
  STAGE IV                17                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
  7P GAIN MUTATED    10  39  90  51
  7P GAIN WILD-TYPE  12  51 105  68
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              10                12
  T2              39                51
  T3              90               105
  T4              51                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"
                   vv
clus                N0 N1 N2 N3
  7P GAIN MUTATED   59 46 41 42
  7P GAIN WILD-TYPE 70 72 43 47
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              59                70
  N1              46                72
  N2              41                43
  N3              42                47
[1] 4 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   175  10
  7P GAIN WILD-TYPE 212  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    175   10
  7P GAIN WILD-TYPE  212   20
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             175               212
  1              10                20
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    62 134
  7P GAIN WILD-TYPE  96 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     62  134
  7P GAIN WILD-TYPE   96  144
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              62                96
  MALE               134               144
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7P GAIN MUTATED                                      23
  7P GAIN WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                       70
  7P GAIN WILD-TYPE                                                     92
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                                  45
  7P GAIN WILD-TYPE                                                                36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  7P GAIN MUTATED                                                 38
  7P GAIN WILD-TYPE                                               40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7P GAIN MUTATED                                                          7
  7P GAIN WILD-TYPE                                                       14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  7P GAIN MUTATED                                                           4
  7P GAIN WILD-TYPE                                                         4
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7P GAIN MUTATED                                          7
  7P GAIN WILD-TYPE                                        6
D13V8, multiclass
                                                                   clus
vv                                                                  7P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         70
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        7
                                                                   clus
vv                                                                  7P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           92
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          6
[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"
D13V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     3 193
  7P GAIN WILD-TYPE   3 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3  193
  7P GAIN WILD-TYPE    3  237
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                3                 3
  YES             193               237
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   161   7   6   9
  7P GAIN WILD-TYPE 186  11  13  16
D13V10, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             161               186
  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"
D13V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED      39                         7
  7P GAIN WILD-TYPE    49                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           1   120
  7P GAIN WILD-TYPE                                         0   154
D13V12, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                                  39                49
  BLACK OR AFRICAN AMERICAN                               7                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 120               154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     3 134
  7P GAIN WILD-TYPE   1 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3  134
  7P GAIN WILD-TYPE    1  179
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO             134               179
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    93  59
  7Q GAIN WILD-TYPE 161  91
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              152               252 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               59                91 
$`7Q GAIN MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6456 
       11.70        11.01         6.97         4.64        18.35        17.29 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 
        9.17        32.78        25.61        18.05        21.11         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       35.24        15.42        18.15        12.76        18.71        14.43 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        12.95         2.20        15.58         7.40 
TCGA-BR-8362 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 
       13.08         0.95         3.32        14.79         0.26         5.39 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A4IY 
       20.22         1.12        16.44         9.86        10.68        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.72         0.53        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 
        1.15         3.25        13.18         0.10         0.16         0.13 
TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 
        0.10        12.43         6.58        12.20        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4469 TCGA-CG-4472 
       15.95         7.99         4.01        14.01         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 
       22.98        36.00        12.03        28.96        79.07        21.07 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 
       12.66        11.93        19.13        18.84        18.54        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 
       10.26        15.22        15.98        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         2.96        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-FP-A8CX TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF 
        0.23        26.47        14.17        24.30        12.30        25.81 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        8.98         0.10        10.19         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP 
       23.84        18.81         3.39         5.19         1.41         6.44 
TCGA-IN-A7NR TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A663 TCGA-R5-A7O7 
        6.51         5.56        60.56        20.15         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV 
       18.21         8.52        61.25         6.08         8.61       122.30 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       57.44         8.94        48.79        13.25        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PY 
       34.45        34.29        46.26         2.50        17.85        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91U 
       65.16        36.69        11.70        11.93        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O 
       36.16         7.36         9.50         2.01         4.54        21.04 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       11.24        40.08        32.94        29.98        54.12        16.14 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

$`7Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4188 
       26.70        19.56         9.47         9.44         6.61         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         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        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       24.76        23.93        28.01        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        3.45         9.07        17.49        11.44         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 
        9.60        20.55         2.66        16.31         6.18        19.50 
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        19.17        15.85         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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
        0.49        11.54        15.81        15.68         8.22        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
       13.51         8.98        14.17        12.82         0.66         0.46 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 
       13.64        11.57         5.13         2.83        13.15         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.07         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 
       11.61         0.10        12.62         3.02         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       54.08        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
        0.00         9.01        18.97        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 
        4.01        69.04         7.99        12.36        20.55        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        13.35        12.79        10.55        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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34         7.40         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8209 TCGA-FP-8210 
       16.24        21.27        11.38        19.53        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       13.58         0.56         5.52        18.08         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       14.27        12.59        11.41        12.10        10.62         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
        5.59        11.84        24.20         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H5 
       21.37        29.98         6.51         6.25         0.26        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       18.38         5.36        13.08         6.74        12.59         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A5UG 
        1.81         7.82        13.51         2.53        37.64         3.72 
TCGA-MX-A5UJ TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       19.73         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 
       37.91        40.64       115.69       116.38        71.38        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       16.87        19.04         5.79         0.92         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PD 
       18.48        27.88        32.48         7.73        28.96        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       22.19        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91K 
       15.65        13.35        26.24        27.35        64.57        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
       18.74        22.68         9.73        52.24         9.04        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U 
        6.58         5.72        64.18         2.66        42.54        22.09 
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        21.11        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 
            14.12             12.43 
[1] "0.1 - 122.3 (14.1)" "0.0 - 116.4 (12.4)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         2        5       17       13        14        17
  7Q GAIN WILD-TYPE       1        9       24       18        24        38
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           2         32         24         19       14
  7Q GAIN WILD-TYPE         2         53         38         22       32
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  2                 1
  STAGE IA                 5                 9
  STAGE IB                17                24
  STAGE II                13                18
  STAGE IIA               14                24
  STAGE IIB               17                38
  STAGE III                2                 2
  STAGE IIIA              32                53
  STAGE IIIB              24                38
  STAGE IIIC              19                22
  STAGE IV                14                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
  7Q GAIN MUTATED     8  36  76  41
  7Q GAIN WILD-TYPE  14  54 119  78
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               8                14
  T2              36                54
  T3              76               119
  T4              41                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"
                   vv
clus                N0 N1 N2 N3
  7Q GAIN MUTATED   52 37 34 36
  7Q GAIN WILD-TYPE 77 81 50 53
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              52                77
  N1              37                81
  N2              34                50
  N3              36                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"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   148   8
  7Q GAIN WILD-TYPE 239  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    148    8
  7Q GAIN WILD-TYPE  239   22
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             148               239
  1               8                22
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    54 114
  7Q GAIN WILD-TYPE 104 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     54  114
  7Q GAIN WILD-TYPE  104  164
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              54               104
  MALE               114               164
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7Q GAIN MUTATED                                      19
  7Q GAIN WILD-TYPE                                    52
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                       62
  7Q GAIN WILD-TYPE                                                    100
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                                  40
  7Q GAIN WILD-TYPE                                                                41
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  7Q GAIN MUTATED                                                 31
  7Q GAIN WILD-TYPE                                               47
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7Q GAIN MUTATED                                                          6
  7Q GAIN WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  7Q GAIN MUTATED                                                           3
  7Q GAIN WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7Q GAIN MUTATED                                          5
  7Q GAIN WILD-TYPE                                        8
D14V8, multiclass
                                                                   clus
vv                                                                  7Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          19
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         62
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        5
                                                                   clus
vv                                                                  7Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          100
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[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"
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2 166
  7Q GAIN WILD-TYPE   4 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  166
  7Q GAIN WILD-TYPE    4  264
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                2                 4
  YES             166               264
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   138   4   5  11
  7Q GAIN WILD-TYPE 209  14  14  14
D14V10, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             138               209
  R1               4                14
  R2               5                14
  RX              11                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED      31                         6
  7Q GAIN WILD-TYPE    57                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           1   104
  7Q GAIN WILD-TYPE                                         0   170
D14V12, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                                  31                57
  BLACK OR AFRICAN AMERICAN                               6                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 104               170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     3 115
  7Q GAIN WILD-TYPE   1 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3  115
  7Q GAIN WILD-TYPE    1  198
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO             115               198
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   110  54
  8P GAIN WILD-TYPE 144  96
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              164               240 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               54                96 
$`8P GAIN MUTATED`
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.01         9.47         6.61         6.97         4.64 
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6565 
       30.90        34.68        15.95        13.87        13.68         9.17 
TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7707 
       19.89        30.90        31.20        32.94        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       15.42         9.07        11.44        12.26         9.60         8.05 
TCGA-BR-8297 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 
        7.40         4.31        14.04         3.32        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8591 
       15.85         5.39         9.21        20.22         9.34        13.45 
TCGA-BR-8676 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J5 
        7.53         7.53        22.26         1.48        13.41        12.82 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5803 
       19.36         0.46        20.42        11.57        13.15         0.07 
TCGA-CD-8530 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MJ 
        0.16         0.10         3.42         9.34         6.58        12.62 
TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
       20.02        15.95        14.01        47.05        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5722 
        0.00        18.97         7.07        12.00        36.00         0.99 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 
       15.02        28.96        79.07        65.10        21.07        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6817 
       11.93        19.13        18.84        17.85        17.19        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV 
       10.55        11.31        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 
       15.16        14.76        11.24        11.31        11.44         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-FP-7829 
        8.38         4.34         0.62        16.24        21.27        19.53 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8245 
        5.52         0.23        18.08        26.47        14.27        12.59 
TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       11.41        24.30        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY 
       22.75        25.81        29.98         8.98         0.10         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        19.36        23.84        12.30         8.88         8.81 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        3.45         3.39         5.19        12.59         6.51         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF 
       60.56        20.15        37.64        19.73         9.86         8.52 
TCGA-R5-A7ZI TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       61.25        16.67       115.69        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
        0.92        48.79         5.46        27.88        28.96        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31        22.19        12.79         2.70         9.27        23.41 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91V 
       26.24        27.35        64.57        36.69        11.93        36.16 
TCGA-VQ-A91W TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U 
        7.36         6.58         5.72        21.04        42.54        22.09 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

$`8P GAIN WILD-TYPE`
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70        19.56         9.44         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
        9.57         6.61        17.29        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        12.16         8.98        21.11 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       12.82         9.21        24.76        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         3.45        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       14.43         0.69        20.55         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         2.20        15.58         6.18        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8371 
        0.26        22.19        17.52         0.95        26.33        11.80 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       14.79         3.72        25.18         1.12        12.79        15.81 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       15.68         8.22        10.68        12.56        13.87         6.08 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
        0.66        13.51        20.65         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 
        2.83         3.25        13.18         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.13         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.13         0.13        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        0.10         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4475 
       54.08         4.01        29.98        19.07         9.01        22.98 
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-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 
       12.03         4.01        69.04         7.99        12.36        20.55 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.54        18.61        13.35        10.26        15.22        15.98 
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        13.71         9.76        15.65 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.40         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-HU-8238 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 
       13.58         0.56         1.51         5.92        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GT 
       10.62         0.76         5.59        11.77        21.37         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
        6.25        10.19        12.95         9.67        27.42        21.21 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.81        18.38         5.36        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.74         1.81         7.82        13.51         2.53         5.56 
TCGA-MX-A5UG TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        3.72        45.67        18.21         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-VQ-A8DV 
      116.38        71.38        57.44         8.94        35.61        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
       13.02        18.48        35.24        21.73        34.45        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
        7.73        46.26         2.50        17.85         1.87        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N 
       13.35        14.33        65.16        11.70        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81        22.68         1.71         9.50         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94P 
        9.04         2.01        55.43         4.54        64.18         2.66 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        40.08        28.41        32.94        29.98 
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        21.11        12.43 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.00              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           115.69            122.30 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            12.79             12.92 
[1] "0.0 - 115.7 (12.8)" "0.1 - 122.3 (12.9)"
[1] "hr=" "1.3"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         1        7       20       12        16        28
  8P GAIN WILD-TYPE       2        7       21       19        22        27
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           1         34         18         17       16
  8P GAIN WILD-TYPE         3         51         44         24       30
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 7                 7
  STAGE IB                20                21
  STAGE II                12                19
  STAGE IIA               16                22
  STAGE IIB               28                27
  STAGE III                1                 3
  STAGE IIIA              34                51
  STAGE IIIB              18                44
  STAGE IIIC              17                24
  STAGE IV                16                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
  8P GAIN MUTATED    11  44  69  49
  8P GAIN WILD-TYPE  11  46 126  70
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              11                11
  T2              44                46
  T3              69               126
  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 45 31 38
  8P GAIN WILD-TYPE 73 73 53 51
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              56                73
  N1              45                73
  N2              31                53
  N3              38                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"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   162  11
  8P GAIN WILD-TYPE 225  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    162   11
  8P GAIN WILD-TYPE  225   19
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             162               225
  1              11                19
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    76 104
  8P GAIN WILD-TYPE  82 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     76  104
  8P GAIN WILD-TYPE   82  174
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              76                82
  MALE               104               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8P GAIN MUTATED                                      31
  8P GAIN WILD-TYPE                                    40
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                       63
  8P GAIN WILD-TYPE                                                     99
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                                  29
  8P GAIN WILD-TYPE                                                                52
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  8P GAIN MUTATED                                                 31
  8P GAIN WILD-TYPE                                               47
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8P GAIN MUTATED                                                         13
  8P GAIN WILD-TYPE                                                        8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  8P GAIN MUTATED                                                           6
  8P GAIN WILD-TYPE                                                         2
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8P GAIN MUTATED                                          6
  8P GAIN WILD-TYPE                                        7
D15V8, multiclass
                                                                   clus
vv                                                                  8P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         63
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        6
                                                                   clus
vv                                                                  8P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            40
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          7
[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"
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     4 176
  8P GAIN WILD-TYPE   2 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4  176
  8P GAIN WILD-TYPE    2  254
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                4                 2
  YES             176               254
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED   140  11   5  15
  8P GAIN WILD-TYPE 207   7  14  10
D15V10, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0             140               207
  R1              11                 7
  R2               5                14
  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      33                         3
  8P GAIN WILD-TYPE    55                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           0   116
  8P GAIN WILD-TYPE                                         1   158
D15V12, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                                  33                55
  BLACK OR AFRICAN AMERICAN                               3                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 116               158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2 129
  8P GAIN WILD-TYPE   2 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2  129
  8P GAIN WILD-TYPE    2  184
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO             129               184
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   138  76
  8Q GAIN WILD-TYPE 116  74
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              214               190 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               76                74 
$`8Q GAIN MUTATED`
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        4.64        30.90        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 
       32.94         9.21        35.24        23.93        15.42        28.01 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        9.07        12.76        11.44         0.69        12.26         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        19.17         0.26        15.85 
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        13.45 
TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
        7.53        16.44         8.22        13.87         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
        1.48        13.41         0.72        12.82        19.36         0.46 
TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 
       11.57        13.15         0.07         0.07         0.07         0.16 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG 
        0.13         0.13         0.10         3.42         9.34         6.58 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       12.62        20.02        15.95         7.99         8.05        54.08 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       14.01        29.98        47.05        12.03        21.99         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5725 
       18.97         7.07        12.00        36.00         0.99        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 
       12.66        11.93        19.13        18.84        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        15.22        15.98        12.79        10.55        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        15.16 
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         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
        8.38         4.34         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       21.27         3.48        19.53         0.56         5.52         0.23 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8610 
       26.47         5.92        14.27        12.59        11.41         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        0.26         2.10        19.36        23.84        12.30         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RO 
        8.81        27.42         3.45         3.39         5.19         1.41 
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         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       20.15        37.64        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N4 
        8.52        61.25        11.05        16.67       115.69        71.38 
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-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       13.25        27.88        28.96        34.29        16.31        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PT 
       12.79         2.70         9.27        23.41        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91V TCGA-VQ-A91W 
       27.35        64.57        36.69        11.93        36.16         7.36 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 
        6.58         5.72        21.04        42.54        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08        12.43        10.62         0.79 

$`8Q GAIN WILD-TYPE`
TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 
       11.70        19.56         7.43        18.35         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
        6.61        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7717 
       18.05         8.98        21.11        12.82        24.76        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73        12.43         3.45        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       14.43        20.55         0.56        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8589 
       11.80        14.79         3.72        25.18         1.12        15.81 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 
        6.28         0.49        11.54        15.81         9.86        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       10.68        12.56         6.08        13.51        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       14.17         0.53         0.66        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
        1.15        13.64         5.13         2.83         3.25        13.18 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
        0.30         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        0.10        11.31        12.43        11.61        12.20         0.10 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4465 
        3.02        27.02         1.02         4.01        19.07         9.01 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 
      105.07        12.03         7.99        12.36        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6527 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       18.61        10.26        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        13.71         9.76 
TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 
        7.40         7.13        14.47        11.38        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8238 
       17.06        59.54         5.03        13.58        18.08         1.51 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GJ 
       14.17        12.10        10.62         5.59        11.77        21.37 
TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI 
       10.19        12.95         9.67        21.21        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        5.36        13.08         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT 
        5.56         3.72         6.08         4.60         9.24         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N5 
        5.13       122.30        37.91        40.64       116.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        8.94        35.61        13.02        18.48        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PK 
       34.45        32.48         7.73        46.26         2.50        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K 
        1.87        15.65        14.33        65.16        11.70        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        20.81        22.68         1.71         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A92D 
       52.24         9.04         2.01        55.43         4.54        64.18 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
        2.66        11.24        28.41        32.94        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       54.12        26.04        16.14        21.11 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.00              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           115.69            122.30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            12.71             13.05 
[1] "0.0 - 115.7 (12.7)" "0.1 - 122.3 (13.1)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         2       11       24       15        18        36
  8Q GAIN WILD-TYPE       1        3       17       16        20        19
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           1         47         25         23       20
  8Q GAIN WILD-TYPE         3         38         37         18       26
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 1
  STAGE IA                11                 3
  STAGE IB                24                17
  STAGE II                15                16
  STAGE IIA               18                20
  STAGE IIB               36                19
  STAGE III                1                 3
  STAGE IIIA              47                38
  STAGE IIIB              25                37
  STAGE IIIC              23                18
  STAGE IV                20                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
  8Q GAIN MUTATED    16  54  95  61
  8Q GAIN WILD-TYPE   6  36 100  58
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              16                 6
  T2              54                36
  T3              95               100
  T4              61                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8Q GAIN MUTATED   71 64 40 47
  8Q GAIN WILD-TYPE 58 54 44 42
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              71                58
  N1              64                54
  N2              40                44
  N3              47                42
[1] 4 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   209  13
  8Q GAIN WILD-TYPE 178  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    209   13
  8Q GAIN WILD-TYPE  178   17
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             209               178
  1              13                17
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    92 142
  8Q GAIN WILD-TYPE  66 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     92  142
  8Q GAIN WILD-TYPE   66  136
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              92                66
  MALE               142               136
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8Q GAIN MUTATED                                      35
  8Q GAIN WILD-TYPE                                    36
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                       85
  8Q GAIN WILD-TYPE                                                     77
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                                  44
  8Q GAIN WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  8Q GAIN MUTATED                                                 42
  8Q GAIN WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8Q GAIN MUTATED                                                         14
  8Q GAIN WILD-TYPE                                                        7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  8Q GAIN MUTATED                                                           6
  8Q GAIN WILD-TYPE                                                         2
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8Q GAIN MUTATED                                          7
  8Q GAIN WILD-TYPE                                        6
D16V8, multiclass
                                                                   clus
vv                                                                  8Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          35
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         85
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        7
                                                                   clus
vv                                                                  8Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            36
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           77
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          6
[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"
D16V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     5 229
  8Q GAIN WILD-TYPE   1 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5  229
  8Q GAIN WILD-TYPE    1  201
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                5                 1
  YES             229               201
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   184  14   6  17
  8Q GAIN WILD-TYPE 163   4  13   8
D16V10, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             184               163
  R1              14                 4
  R2               6                13
  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                         6
  8Q GAIN WILD-TYPE    43                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           0   149
  8Q GAIN WILD-TYPE                                         1   125
D16V12, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                                  45                43
  BLACK OR AFRICAN AMERICAN                               6                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 149               125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3 171
  8Q GAIN WILD-TYPE   1 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  171
  8Q GAIN WILD-TYPE    1  142
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO             171               142
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    40  15
  9P GAIN WILD-TYPE 214 135
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               55               349 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               15               135 
$`9P GAIN MUTATED`
TCGA-B7-A5TK TCGA-BR-6456 TCGA-BR-6707 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
        9.47        17.29        19.89        23.93        15.42        18.15 
TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8588 TCGA-BR-8682 
       18.71         9.60         2.66         2.20        12.79        16.44 
TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8535 
        0.53         0.46        20.42         2.83        13.18         0.13 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4444 TCGA-CG-4477 TCGA-D7-6528 TCGA-D7-6818 
       12.20         7.99        47.05        30.97        15.22        10.55 
TCGA-D7-6822 TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-A8CX 
       12.33        14.76        11.44         0.62        21.27         0.23 
TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP 
       18.08        14.17         0.76        12.30        22.75         8.98 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-8663 TCGA-IN-A6RP TCGA-KB-A6F7 
        2.10        12.95        12.30         3.39         6.44        60.56 
TCGA-KB-A93G TCGA-R5-A7ZI TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DU 
       20.15        61.25       122.30       115.69        35.61         5.46 
TCGA-VQ-A8PC TCGA-VQ-A8PP TCGA-VQ-A91S TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 
       46.26        23.41        22.68        52.24         9.04         5.72 
TCGA-VQ-AA6F 
       54.12 

$`9P GAIN WILD-TYPE`
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-4267 
        6.97         4.64         7.43        18.35        30.90         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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7716 
       32.94        12.82         9.21        24.76        35.24        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       17.49        14.43        11.44         0.69        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        12.95        16.31        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        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 
       19.17        14.79         0.26        15.85         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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
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        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       19.36        13.51        20.65         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         3.25        13.15         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58         0.10        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-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         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-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        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-D7-8575 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-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        15.16        13.78        13.71        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
        9.76         2.96        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         7.99        16.24        14.47        72.23        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-HJ-7597 TCGA-HU-8238 
        5.03        13.58         0.56         5.52        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       24.30         5.59        11.84        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         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
       10.19         0.26        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
        8.81        27.42        21.21         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19        13.08         1.41         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
        5.56        37.64         3.72        19.73         9.86        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        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       11.93        61.22        18.74        20.81         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36         9.50         9.73         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58        64.18        21.04         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       22.09        18.41        40.08        28.41        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        26.04        16.14        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.13              0.00 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           122.30            116.38 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            13.18             12.79 
[1] "0.1 - 122.3 (13.2)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.6"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         1        2        9        3         5         8
  9P GAIN WILD-TYPE       2       12       32       28        33        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           0         10          7          5        7
  9P GAIN WILD-TYPE         4         75         55         36       39
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 2                12
  STAGE IB                 9                32
  STAGE II                 3                28
  STAGE IIA                5                33
  STAGE IIB                8                47
  STAGE III                0                 4
  STAGE IIIA              10                75
  STAGE IIIB               7                55
  STAGE IIIC               5                36
  STAGE IV                 7                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
  9P GAIN MUTATED     6  15  20  17
  9P GAIN WILD-TYPE  16  75 175 102
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               6                16
  T2              15                75
  T3              20               175
  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
  9P GAIN MUTATED    19  19   8  12
  9P GAIN WILD-TYPE 110  99  76  77
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              19               110
  N1              19                99
  N2               8                76
  N3              12                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"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    55   3
  9P GAIN WILD-TYPE 332  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     55    3
  9P GAIN WILD-TYPE  332   27
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              55               332
  1               3                27
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    21  38
  9P GAIN WILD-TYPE 137 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     21   38
  9P GAIN WILD-TYPE  137  240
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              21               137
  MALE                38               240
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9P GAIN MUTATED                                       8
  9P GAIN WILD-TYPE                                    63
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                       18
  9P GAIN WILD-TYPE                                                    144
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                                   7
  9P GAIN WILD-TYPE                                                                74
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  9P GAIN MUTATED                                                 12
  9P GAIN WILD-TYPE                                               66
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9P GAIN MUTATED                                                          8
  9P GAIN WILD-TYPE                                                       13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  9P GAIN MUTATED                                                           3
  9P GAIN WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9P GAIN MUTATED                                          3
  9P GAIN WILD-TYPE                                       10
D17V8, multiclass
                                                                   clus
vv                                                                  9P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  9P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          144
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                74
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 66
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         10
[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"
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  57
  9P GAIN WILD-TYPE   4 373
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   57
  9P GAIN WILD-TYPE    4  373
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                2                 4
  YES              57               373
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    50   3   1   2
  9P GAIN WILD-TYPE 297  15  18  23
D17V10, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              50               297
  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                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           0    34
  9P GAIN WILD-TYPE                                         1   240
D17V12, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                                  15                73
  BLACK OR AFRICAN AMERICAN                               1                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  34               240
[1] 4 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   2 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   41
  9P GAIN WILD-TYPE    2  272
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              41               272
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    47  25
  9Q GAIN WILD-TYPE 207 125
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               72               332 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               25               125 
$`9Q GAIN MUTATED`
TCGA-B7-A5TK TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6707 TCGA-BR-7704 TCGA-BR-7707 
        9.47        18.35        17.29        19.89        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8295 
       15.42        18.15        18.71         9.60         2.66         2.20 
TCGA-BR-8360 TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4J9 
        6.18        12.79        16.44        22.26         0.53         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8535 TCGA-CG-4436 
       20.65        20.42         2.83        13.18         0.13         7.99 
TCGA-CG-4444 TCGA-CG-4477 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 
       47.05        30.97        12.66        17.19        15.22        10.55 
TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A747 TCGA-EQ-5647 
       14.27        14.76        11.44        15.65         8.38         0.62 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8249 
       21.27         3.48         0.23        18.08         1.51        14.17 
TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H5 TCGA-IN-7808 
        0.76        12.30        22.75         8.98        12.30         3.45 
TCGA-IN-8663 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-KB-A93G TCGA-R5-A7ZI 
        3.39         1.41         6.44        60.56        20.15        61.25 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PC 
      122.30       115.69        35.61        48.79         5.46        46.26 
TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91X 
       23.41        27.35        18.74        22.68        36.16         9.50 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A94T TCGA-VQ-AA6F TCGA-VQ-AA6K 
       52.24         9.04         5.72        11.24        54.12        12.43 

$`9Q GAIN WILD-TYPE`
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-4201 TCGA-BR-4267 TCGA-BR-4279 
        6.97         4.64         7.43        30.90         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-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       12.82         9.21        24.76        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45         9.07        12.76        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        12.26        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 
       12.95        16.31        15.58         7.40        19.50        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        15.81         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        12.56        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI 
       12.82         0.66        19.36        13.51         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13         3.25        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        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 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        22.98         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.36        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
       18.54        18.61        17.85        13.35        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        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-A4YU 
       17.19        18.21        14.66        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        15.16        13.78        13.71        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
        9.76         2.96         4.34         7.40         7.13         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 
       16.24        14.47        72.23        11.38        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-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
        5.52        26.47         5.92        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       12.10        10.62        24.30         5.59        11.84        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-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       19.36        23.84         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       21.21        18.81        18.38         5.36         5.19        13.08 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53         5.56        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
        9.86        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-A8MW 
        9.24        11.05         8.61         5.13        16.67        37.91 
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-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       19.04         5.79         0.92        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70        17.85         1.87         9.27        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       26.24        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       11.93        61.22        20.81         1.71         7.36         9.73 
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        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        29.98        17.13        26.04        16.14        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.13              0.00 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           122.30            116.38 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           14.515            12.775 
[1] "0.1 - 122.3 (14.5)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.3"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         1        3       10        4         5        10
  9Q GAIN WILD-TYPE       2       11       31       27        33        45
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           1         18          9          5        8
  9Q GAIN WILD-TYPE         3         67         53         36       38
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 3                11
  STAGE IB                10                31
  STAGE II                 4                27
  STAGE IIA                5                33
  STAGE IIB               10                45
  STAGE III                1                 3
  STAGE IIIA              18                67
  STAGE IIIB               9                53
  STAGE IIIC               5                36
  STAGE IV                 8                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
  9Q GAIN MUTATED     7  17  30  21
  9Q GAIN WILD-TYPE  15  73 165  98
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               7                15
  T2              17                73
  T3              30               165
  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  24  14  15
  9Q GAIN WILD-TYPE 106  94  70  74
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              23               106
  N1              24                94
  N2              14                70
  N3              15                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"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    71   4
  9Q GAIN WILD-TYPE 316  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     71    4
  9Q GAIN WILD-TYPE  316   26
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              71               316
  1               4                26
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    24  53
  9Q GAIN WILD-TYPE 134 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     24   53
  9Q GAIN WILD-TYPE  134  225
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              24               134
  MALE                53               225
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9Q GAIN MUTATED                                       9
  9Q GAIN WILD-TYPE                                    62
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                       24
  9Q GAIN WILD-TYPE                                                    138
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                                  11
  9Q GAIN WILD-TYPE                                                                70
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  9Q GAIN MUTATED                                                 18
  9Q GAIN WILD-TYPE                                               60
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9Q GAIN MUTATED                                                          8
  9Q GAIN WILD-TYPE                                                       13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  9Q GAIN MUTATED                                                           3
  9Q GAIN WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9Q GAIN MUTATED                                          4
  9Q GAIN WILD-TYPE                                        9
D18V8, multiclass
                                                                   clus
vv                                                                  9Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        4
                                                                   clus
vv                                                                  9Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                70
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 60
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          9
[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"
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  75
  9Q GAIN WILD-TYPE   4 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   75
  9Q GAIN WILD-TYPE    4  355
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                2                 4
  YES              75               355
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    66   4   1   3
  9Q GAIN WILD-TYPE 281  14  18  22
D18V10, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              66               281
  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                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           0    47
  9Q GAIN WILD-TYPE                                         1   227
D18V12, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                                  15                73
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  47               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"
D18V13, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  52
  9Q GAIN WILD-TYPE   2 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   52
  9Q GAIN WILD-TYPE    2  261
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              52               261
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    56  36
  10P GAIN WILD-TYPE 198 114
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                92                312 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                36                114 
$`10P GAIN MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 
        6.61        17.29        13.68         9.17        21.11         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8077 
       35.24        15.42        28.01        18.15        28.73         0.69 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        9.60        12.95         2.66         2.20        15.58         7.40 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A4J1 TCGA-BR-A4J7 
        5.39         9.21        16.44         9.86         0.72        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8524 
       13.51        20.65         1.15        13.64        13.18         0.07 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4300 
        0.07         0.16         9.34        12.43        11.61        20.02 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5730 
        4.01        47.05        21.99        12.00        30.97         4.01 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-8578 
       19.13        20.55        18.84        17.19        10.55        21.14 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 
       16.44        11.31        15.65         7.40         0.62        72.23 
TCGA-FP-7735 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 
        3.48         1.51         5.92        11.41         0.76        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 
       24.20        22.75        25.81        11.77         6.25        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A7NR 
       23.84         9.67        27.42         3.45         3.39         6.51 
TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 
       37.64        18.21         6.08        11.05         8.61        16.67 
TCGA-RD-A8MV TCGA-VQ-A8DU TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH 
      122.30         5.46        21.73         7.73        46.26        12.79 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91U TCGA-VQ-A925 TCGA-VQ-A94O 
       64.57        14.33        11.93         1.71         4.54        21.04 
TCGA-VQ-A94U TCGA-VQ-AA6J 
       22.09        21.11 

$`10P GAIN WILD-TYPE`
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-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 
        9.57         6.61        34.68        15.95        13.87        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-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        30.90        31.20        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       24.76        23.93        15.32        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       12.76        18.71        17.49        14.43        11.44        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 
       20.55         8.05         0.56        16.31         6.18        19.50 
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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
        0.26        15.85         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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        0.49        11.54        15.81        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       12.82         0.66         0.46        20.42        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
        2.83         3.25        13.15         0.30         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.10         0.13         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.10         3.42        11.31         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        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-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
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-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        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        12.36        12.66        11.93 
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-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        14.66        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44         9.76         2.96         8.38         4.34         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
        7.99        16.24        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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 
        0.56         5.52         0.23        18.08        26.47        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       12.59        14.17        12.10        10.62        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       11.84         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        10.19         0.26         2.10        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.88         8.81        21.21        18.81        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         6.44         6.74        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        5.56         1.81         7.82        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       60.56        20.15         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A8MW 
        8.52        61.25         4.60         9.24         5.13        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-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        18.48        35.24        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       32.48        28.96        34.29        16.31        22.19         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-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       13.35        26.24        27.35        65.16        36.69        11.70 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        18.74        20.81        22.68        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        52.24         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58         5.72        64.18         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        40.08        28.41        32.94        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        12.43        10.62         0.79 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.07               0.00 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            122.30             116.38 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            12.610             12.855 
[1] "0.1 - 122.3 (12.6)" "0.0 - 116.4 (12.9)"
[1] "hr=" "1.1"
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       3        8       35       26        30        39
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           2         22         14          7       10
  10P GAIN WILD-TYPE         2         63         48         34       36
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  6                  8
  STAGE IB                  6                 35
  STAGE II                  5                 26
  STAGE IIA                 8                 30
  STAGE IIB                16                 39
  STAGE III                 2                  2
  STAGE IIIA               22                 63
  STAGE IIIB               14                 48
  STAGE IIIC                7                 34
  STAGE IV                 10                 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 GAIN MUTATED     5  15  51  26
  10P GAIN WILD-TYPE  17  75 144  93
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                5                 17
  T2               15                 75
  T3               51                144
  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   32 22 22 19
  10P GAIN WILD-TYPE 97 96 62 70
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               32                 97
  N1               22                 96
  N2               22                 62
  N3               19                 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"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    88   7
  10P GAIN WILD-TYPE 299  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     88    7
  10P GAIN WILD-TYPE  299   23
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               88                299
  1                7                 23
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    38  60
  10P GAIN WILD-TYPE 120 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     38   60
  10P GAIN WILD-TYPE  120  218
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               38                120
  MALE                 60                218
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10P GAIN MUTATED                                      13
  10P GAIN WILD-TYPE                                    58
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                       34
  10P GAIN WILD-TYPE                                                    128
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                                  19
  10P GAIN WILD-TYPE                                                                62
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  10P GAIN MUTATED                                                 25
  10P GAIN WILD-TYPE                                               53
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10P GAIN MUTATED                                                          3
  10P GAIN WILD-TYPE                                                       18
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  10P GAIN MUTATED                                                           1
  10P GAIN WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10P GAIN MUTATED                                          2
  10P GAIN WILD-TYPE                                       11
D19V8, multiclass
                                                                   clus
vv                                                                  10P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  10P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          11
[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"
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2  96
  10P GAIN WILD-TYPE   4 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   96
  10P GAIN WILD-TYPE    4  334
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                  4
  YES               96                334
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    80   2   6   5
  10P GAIN WILD-TYPE 267  16  13  20
D19V10, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               80                267
  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      27                         5
  10P GAIN WILD-TYPE    61                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           1    55
  10P GAIN WILD-TYPE                                         0   219
D19V12, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                                   27                 61
  BLACK OR AFRICAN AMERICAN                                5                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   55                219
[1] 4 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   4 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   75
  10P GAIN WILD-TYPE    4  238
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               75                238
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    39  27
  10Q GAIN WILD-TYPE 215 123
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                66                338 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                27                123 
$`10Q GAIN MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
        6.61        17.29        26.10         9.21        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
       28.01        28.73         0.69        12.95         2.66        15.58 
TCGA-BR-8297 TCGA-BR-8682 TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF 
        7.40        16.44         0.72        19.36        20.65         1.15 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 
       13.18         0.07         0.07         0.16         0.13        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4477 TCGA-D7-6519 TCGA-D7-6520 
       47.05        21.99        12.00        30.97        20.55        18.84 
TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV 
       17.19        10.55        18.21        21.14        16.44        11.24 
TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 TCGA-HU-8238 
       11.31         7.40         0.62        72.23         3.48         1.51 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4H4 
       11.41         0.76        12.30        24.20        22.75        23.84 
TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8663 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS 
        9.67         3.45         3.39        18.21         6.08        11.05 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PX 
        8.61       122.30        21.73        46.26        12.79        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94U 
       14.33        11.93        20.81         4.54         5.72        22.09 

$`10Q GAIN WILD-TYPE`
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-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       32.94        12.82        24.76        23.93        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        0.56        16.31         2.20         6.18        19.50        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        15.81         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        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        12.82         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        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
       13.15         0.30         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        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-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         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-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        11.93        19.13        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       13.35        10.26        15.22        15.98        12.79        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       13.71        11.44         9.76         2.96        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 
        4.34         7.13         7.99        16.24        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       26.47         5.92        14.27        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GF 
       10.62        24.30         5.59        11.84         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 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       12.30         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.38         5.36         5.19        13.08         1.41         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         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
       13.51         2.53         5.56        60.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73         9.86        45.67         8.52        61.25 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
        4.60         9.24         5.13        16.67        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-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        18.48        35.24        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       32.48         7.73        28.96        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        26.24        27.35        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.70        61.22        18.74        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        7.36         9.50         9.73        52.24         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58        64.18        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        40.08        28.41        32.94        29.98 
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        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.07               0.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            122.30             116.38 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            13.065             12.805 
[1] "0.1 - 122.3 (13.1)" "0.0 - 116.4 (12.8)"
[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        11
  10Q GAIN WILD-TYPE       3        9       37       25        36        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           2         19         10          2        8
  10Q GAIN WILD-TYPE         2         66         52         39       38
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  5                  9
  STAGE IB                  4                 37
  STAGE II                  6                 25
  STAGE IIA                 2                 36
  STAGE IIB                11                 44
  STAGE III                 2                  2
  STAGE IIIA               19                 66
  STAGE IIIB               10                 52
  STAGE IIIC                2                 39
  STAGE IV                  8                 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
  10Q GAIN MUTATED     4  12  37  16
  10Q GAIN WILD-TYPE  18  78 158 103
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                4                 18
  T2               12                 78
  T3               37                158
  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
  10Q GAIN MUTATED    22  15  20  11
  10Q GAIN WILD-TYPE 107 103  64  78
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               22                107
  N1               15                103
  N2               20                 64
  N3               11                 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    64   4
  10Q GAIN WILD-TYPE 323  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     64    4
  10Q GAIN WILD-TYPE  323   26
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               64                323
  1                4                 26
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    29  41
  10Q GAIN WILD-TYPE 129 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     29   41
  10Q GAIN WILD-TYPE  129  237
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               29                129
  MALE                 41                237
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10Q GAIN MUTATED                                       9
  10Q GAIN WILD-TYPE                                    62
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                       24
  10Q GAIN WILD-TYPE                                                    138
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                                  12
  10Q GAIN WILD-TYPE                                                                69
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  10Q GAIN MUTATED                                                 18
  10Q GAIN WILD-TYPE                                               60
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10Q GAIN MUTATED                                                          2
  10Q GAIN WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  10Q GAIN MUTATED                                                           2
  10Q GAIN WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10Q GAIN MUTATED                                          2
  10Q GAIN WILD-TYPE                                       11
D20V8, multiclass
                                                                   clus
vv                                                                  10Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  10Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  60
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          11
[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"
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  68
  10Q GAIN WILD-TYPE   4 362
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   68
  10Q GAIN WILD-TYPE    4  362
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 2                  4
  YES               68                362
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    58   1   4   4
  10Q GAIN WILD-TYPE 289  17  15  21
D20V10, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               58                289
  R1                1                 17
  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"
D20V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED      16                         3
  10Q GAIN WILD-TYPE    72                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           1    42
  10Q GAIN WILD-TYPE                                         0   232
D20V12, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                                   16                 72
  BLACK OR AFRICAN AMERICAN                                3                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   42                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"
D20V13, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0  54
  10Q GAIN WILD-TYPE   4 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   54
  10Q GAIN WILD-TYPE    4  259
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               54                259
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    35  23
  11P GAIN WILD-TYPE 219 127
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                58                346 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                23                127 
$`11P GAIN MUTATED`
TCGA-B7-A5TJ TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 
       11.01        13.87        35.24         3.45        17.49        11.44 
TCGA-BR-8296 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J8 
       15.58        11.54        15.68        22.26        12.89        13.51 
TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 
        0.07         0.10         9.34        12.20        20.02        54.08 
TCGA-CG-5722 TCGA-D7-6526 TCGA-D7-8576 TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7916 
        0.99        17.19        14.66         2.96         7.99        14.07 
TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-A4G2 TCGA-HU-A4HD TCGA-IN-A6RJ 
       17.06         0.23         5.92        24.30        27.42         5.36 
TCGA-IN-A6RO TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZI 
        1.41         5.56         1.81         5.56        37.64        61.25 
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        35.24        22.19         2.70        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       14.33        18.74        22.68         1.71         9.50         9.73 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       40.08        32.94        29.98        54.12 

$`11P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
        9.07        12.76        18.71        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         2.20         7.40         6.18        19.50        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        7.53         0.49        15.81        16.44         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        12.56        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 
       13.41        13.51         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 
       12.82         0.66        19.36         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        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         3.42        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58         0.10        12.62         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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       18.97         7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        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        12.36        12.66        11.93        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-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62        16.24        14.47        72.23        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-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
        0.56         5.52        18.08        26.47         1.51        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        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         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       21.21         3.45        18.81         3.39        18.38         5.19 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
       13.08         6.44         6.74        12.59         6.51         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        60.56        20.15         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
        9.86        45.67        18.21         8.52         6.08         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-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
      116.38        71.38        57.44        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        0.92        48.79        13.25        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        26.24        27.35        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W 
       11.70        11.93        61.22        20.81        36.16         7.36 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       52.24         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        64.18        21.04         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       22.09        18.41        28.41        17.13        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.07               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            115.69             122.30 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            13.970             12.775 
[1] "0.1 - 115.7 (14.0)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         0        2        5        2         2        10
  11P GAIN WILD-TYPE       3       12       36       29        36        45
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           0         13         11          8        8
  11P GAIN WILD-TYPE         4         72         51         33       38
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  2                 12
  STAGE IB                  5                 36
  STAGE II                  2                 29
  STAGE IIA                 2                 36
  STAGE IIB                10                 45
  STAGE III                 0                  4
  STAGE IIIA               13                 72
  STAGE IIIB               11                 51
  STAGE IIIC                8                 33
  STAGE IV                  8                 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
  11P GAIN MUTATED     3   7  31  20
  11P GAIN WILD-TYPE  19  83 164  99
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                3                 19
  T2                7                 83
  T3               31                164
  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
  11P GAIN MUTATED    12  17  19  13
  11P GAIN WILD-TYPE 117 101  65  76
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               12                117
  N1               17                101
  N2               19                 65
  N3               13                 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"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    56   4
  11P GAIN WILD-TYPE 331  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     56    4
  11P GAIN WILD-TYPE  331   26
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               56                331
  1                4                 26
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    24  40
  11P GAIN WILD-TYPE 134 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     24   40
  11P GAIN WILD-TYPE  134  238
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               24                134
  MALE                 40                238
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11P GAIN MUTATED                                       7
  11P GAIN WILD-TYPE                                    64
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                       22
  11P GAIN WILD-TYPE                                                    140
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                                  17
  11P GAIN WILD-TYPE                                                                64
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  11P GAIN MUTATED                                                 15
  11P GAIN WILD-TYPE                                               63
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11P GAIN MUTATED                                                          1
  11P GAIN WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  11P GAIN MUTATED                                                           0
  11P GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11P GAIN MUTATED                                          2
  11P GAIN WILD-TYPE                                       11
D21V8, multiclass
                                                                   clus
vv                                                                  11P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  11P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  63
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          11
[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"
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  63
  11P GAIN WILD-TYPE   5 367
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   63
  11P GAIN WILD-TYPE    5  367
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 1                  5
  YES               63                367
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    49   2   5   4
  11P GAIN WILD-TYPE 298  16  14  21
D21V10, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               49                298
  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                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           1    37
  11P GAIN WILD-TYPE                                         0   237
D21V12, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                3                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   37                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"
D21V13, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  40
  11P GAIN WILD-TYPE   3 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   40
  11P GAIN WILD-TYPE    3  273
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               40                273
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    42  26
  11Q GAIN WILD-TYPE 212 124
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                68                336 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                26                124 
$`11Q GAIN MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8058 
       11.01         9.44        13.87        35.24         3.45        17.49 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8589 TCGA-BR-8686 
       11.44         0.69        15.58        19.50        15.81        15.68 
TCGA-BR-A4IY TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 
       12.89         0.07         0.10         9.34        12.20        20.02 
TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5722 TCGA-D7-6526 
       54.08        47.05        12.00        30.97         0.99        17.19 
TCGA-D7-6528 TCGA-D7-8576 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-F1-6875 
       15.22        14.66        11.24         2.96         7.99        72.23 
TCGA-FP-8099 TCGA-HU-8243 TCGA-HU-A4G2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 
       17.06         5.92        24.30        12.30        27.42         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 
        5.36         1.41         6.74         5.56         1.81         5.56 
TCGA-KB-A93H TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
       37.64        61.25         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        35.24        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        11.93        18.74        22.68 
TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        1.71         9.73         4.54        40.08        32.94        29.98 
TCGA-VQ-AA6F TCGA-ZQ-A9CR 
       54.12         0.79 

$`11Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        19.56         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       28.01        18.15        15.32        28.73        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       12.76        18.71        14.43        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        12.95         2.66        16.31         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 
       19.17        14.79         0.26        15.85         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 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
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        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        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 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         3.42        11.31        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        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        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.85        13.35        10.26        15.98        12.79        10.55 
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-A6EX TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62        16.24        14.47        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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        23.84         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       21.21         3.45        18.81        18.38         5.19        13.08 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.44        12.59         6.51         7.82        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       60.56        20.15         3.72        19.73         9.86        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-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-A8DT 
       57.44        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        16.31         2.50        12.79 
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-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       26.24        27.35        65.16        36.69        11.70        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       20.81        36.16         7.36         9.50        52.24         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        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 
        2.66        42.54        11.24        22.09        18.41        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        26.04        16.14        21.11        12.43        10.62 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.07               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            115.69             122.30 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            13.445             12.790 
[1] "0.1 - 115.7 (13.4)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         0        3        7        2         2        13
  11Q GAIN WILD-TYPE       3       11       34       29        36        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           0         15         12          8        9
  11Q GAIN WILD-TYPE         4         70         50         33       37
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  3                 11
  STAGE IB                  7                 34
  STAGE II                  2                 29
  STAGE IIA                 2                 36
  STAGE IIB                13                 42
  STAGE III                 0                  4
  STAGE IIIA               15                 70
  STAGE IIIB               12                 50
  STAGE IIIC                8                 33
  STAGE IV                  9                 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 GAIN MUTATED     3  13  31  24
  11Q GAIN WILD-TYPE  19  77 164  95
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                3                 19
  T2               13                 77
  T3               31                164
  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 113  98  61  78
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               16                113
  N1               20                 98
  N2               23                 61
  N3               11                 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"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    67   4
  11Q GAIN WILD-TYPE 320  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     67    4
  11Q GAIN WILD-TYPE  320   26
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               67                320
  1                4                 26
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    30  44
  11Q GAIN WILD-TYPE 128 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     30   44
  11Q GAIN WILD-TYPE  128  234
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               30                128
  MALE                 44                234
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11Q GAIN MUTATED                                       7
  11Q GAIN WILD-TYPE                                    64
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                       26
  11Q GAIN WILD-TYPE                                                    136
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                                  18
  11Q GAIN WILD-TYPE                                                                63
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  11Q GAIN MUTATED                                                 19
  11Q GAIN WILD-TYPE                                               59
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11Q GAIN MUTATED                                                          1
  11Q GAIN WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  11Q GAIN MUTATED                                                           1
  11Q GAIN WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11Q GAIN MUTATED                                          1
  11Q GAIN WILD-TYPE                                       12
D22V8, multiclass
                                                                   clus
vv                                                                  11Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  11Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           136
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          12
[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"
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  73
  11Q GAIN WILD-TYPE   5 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   73
  11Q GAIN WILD-TYPE    5  357
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 1                  5
  YES               73                357
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    58   2   6   4
  11Q GAIN WILD-TYPE 289  16  13  21
D22V10, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               58                289
  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                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           1    43
  11Q GAIN WILD-TYPE                                         0   231
D22V12, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                4                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   43                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"
D22V13, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  46
  11Q GAIN WILD-TYPE   3 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   46
  11Q GAIN WILD-TYPE    3  267
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               46                267
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    59  26
  12P GAIN WILD-TYPE 195 124
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                85                319 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                26                124 
$`12P GAIN MUTATED`
TCGA-B7-A5TK TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-7723 
        9.47        39.12        32.78        12.16        21.11        28.73 
TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 
       18.71        12.26         2.20        19.50         0.26         0.95 
TCGA-BR-8370 TCGA-BR-8381 TCGA-BR-8486 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF 
        3.32         0.26        20.22         1.48         0.72         1.15 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CG-4444 
        2.83         3.25         0.07         0.16         0.10        47.05 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-5578 
       21.99        22.98         0.99        12.03        79.07        12.66 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A4YV 
       19.13        18.54        17.19        11.31        19.50         5.92 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-A4SO 
       11.31         2.96        15.65         8.38         7.40        16.24 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-A4BF TCGA-HU-8238 
       11.38         3.48        19.53        22.29         5.52         1.51 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       14.17        12.10        24.30         3.25        22.75        25.81 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4HD TCGA-IN-7808 
        8.98         6.51         6.25        10.19        27.42         3.45 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-AB1V TCGA-IP-7968 
        3.39         5.36         6.44         6.74         7.82         2.53 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A8N6 
       60.56        37.64        18.21        61.25         6.08         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P5 
        5.79        48.79        13.25        18.48        21.73         7.73 
TCGA-VQ-A8PE TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A928 
       22.19        36.69        11.93        20.81        36.16         5.72 
TCGA-VQ-AA6K 
       12.43 

$`12P GAIN WILD-TYPE`
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-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       13.68        19.33        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        12.43         3.45         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43        11.44         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        8.05         0.56        12.95         2.66        16.31        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        7.40         6.18        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        19.17        14.79        15.85 
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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        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 
       12.82         0.66        19.36        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 
       20.42        13.64        11.57         5.13        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
        0.30         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.10         0.13         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        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 
        0.10        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-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-D7-5579 
        4.01        69.04        21.07         7.99        12.36        11.93 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       20.55        18.84        18.61        17.85        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        10.55        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        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       11.24        11.44         9.76         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-8099 
        7.99        14.47        72.23        21.27        14.07        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       26.47         5.92        14.27        12.59        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH 
        0.76         5.59        12.30        11.84        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 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
       21.21        18.81        18.38         5.19        13.08         1.41 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 
       12.59         6.51         5.56         1.81        13.51         5.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       20.15         3.72        19.73         9.86        45.67         8.52 
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-A8DU 
       57.44        35.61        16.87        19.04         0.92         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.02        35.24        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        46.26        16.31         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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       26.24        27.35        64.57        14.33        65.16        11.70 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        18.74        22.68         1.71         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        52.24         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58        64.18        21.04         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       22.09        18.41        40.08        28.41        32.94        29.98 
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        21.11        10.62 
TCGA-ZQ-A9CR 
        0.79 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.07               0.00 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             79.07             122.30 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             11.93              13.08 
[1] "0.1 - 79.1 (11.9)"  "0.0 - 122.3 (13.1)"
[1] "hr=" "1.2"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         0        2        7        4        12        14
  12P GAIN WILD-TYPE       3       12       34       27        26        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           2         22         11          7        8
  12P GAIN WILD-TYPE         2         63         51         34       38
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  2                 12
  STAGE IB                  7                 34
  STAGE II                  4                 27
  STAGE IIA                12                 26
  STAGE IIB                14                 41
  STAGE III                 2                  2
  STAGE IIIA               22                 63
  STAGE IIIB               11                 51
  STAGE IIIC                7                 34
  STAGE IV                  8                 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
  12P GAIN MUTATED     5  13  52  19
  12P GAIN WILD-TYPE  17  77 143 100
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                5                 17
  T2               13                 77
  T3               52                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    25  23  24  16
  12P GAIN WILD-TYPE 104  95  60  73
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               25                104
  N1               23                 95
  N2               24                 60
  N3               16                 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"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    79   6
  12P GAIN WILD-TYPE 308  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     79    6
  12P GAIN WILD-TYPE  308   24
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               79                308
  1                6                 24
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    31  58
  12P GAIN WILD-TYPE 127 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     31   58
  12P GAIN WILD-TYPE  127  220
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               31                127
  MALE                 58                220
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12P GAIN MUTATED                                      17
  12P GAIN WILD-TYPE                                    54
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                       28
  12P GAIN WILD-TYPE                                                    134
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                                  14
  12P GAIN WILD-TYPE                                                                67
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  12P GAIN MUTATED                                                 21
  12P GAIN WILD-TYPE                                               57
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12P GAIN MUTATED                                                          5
  12P GAIN WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  12P GAIN MUTATED                                                           1
  12P GAIN WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12P GAIN MUTATED                                          2
  12P GAIN WILD-TYPE                                       11
D23V8, multiclass
                                                                   clus
vv                                                                  12P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  12P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          11
[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"
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  89
  12P GAIN WILD-TYPE   6 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   89
  12P GAIN WILD-TYPE    6  341
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 0                  6
  YES               89                341
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    74   4   4   1
  12P GAIN WILD-TYPE 273  14  15  24
D23V10, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               74                273
  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                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           0    55
  12P GAIN WILD-TYPE                                         1   219
D23V12, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                                   20                 68
  BLACK OR AFRICAN AMERICAN                                3                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   55                219
[1] 4 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  66
  12P GAIN WILD-TYPE   2 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   66
  12P GAIN WILD-TYPE    2  247
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               66                247
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    50  24
  12Q GAIN WILD-TYPE 204 126
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                74                330 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                24                126 
$`12Q GAIN MUTATED`
TCGA-B7-A5TK TCGA-BR-4267 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-7723 
        9.47         6.18        39.12        32.78        12.16        28.73 
TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 
       18.71        12.26         2.20         0.26         0.95         3.32 
TCGA-BR-8381 TCGA-BR-8589 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-CD-5798 
        0.26        15.81         1.48         0.72         0.53         2.83 
TCGA-CD-5799 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A48A 
        3.25         0.07         0.16         0.13         9.34        12.43 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5727 TCGA-D7-5578 
       47.05        21.99        12.00         0.99        79.07        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         7.40        11.38        14.07        22.29         5.52 
TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD 
        1.51        14.17        12.10        24.30         3.25        22.75 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4HD 
        8.98         6.51         6.25        10.19        23.84        27.42 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 
        3.45         3.39         5.36         7.82         2.53        60.56 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8P5 
       61.25         6.08         8.94         5.79        48.79         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91V 
       22.19         2.70        14.33        11.93        20.81        36.16 
TCGA-VQ-A91X TCGA-VQ-A928 
        9.50         5.72 

$`12Q GAIN WILD-TYPE`
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-4279 
        6.97         4.64         7.43        18.35        30.90         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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        12.43         3.45         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43        11.44         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        8.05         0.56        12.95         2.66        16.31        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50        13.08        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31        14.04        11.80        19.17        14.79 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         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        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
       22.26        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.82         0.66        19.36        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5800 
       20.42         1.15        13.64        11.57         5.13        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 
        0.10         0.13         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        3.42        11.31        11.61         6.58        12.20         0.10 
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-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        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        12.36        11.93 
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        10.55        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        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        4.34         7.13         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 
       72.23        21.27         3.48        19.53        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         0.23        18.08        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        14.27        12.59        11.41        10.62         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GH 
        5.59        12.30        11.84        24.20        25.81        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-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.81        18.38         5.19        13.08         1.41         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         5.56         1.81        13.51 
TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        20.15        37.64         3.72        19.73         9.86 
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-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-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       19.04         0.92         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-A8P8 
       35.24        21.73        34.45        27.88        32.48        28.96 
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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       27.35        64.57        65.16        36.69        11.70        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       18.74        22.68         1.71         7.36         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.04         2.01        55.43         4.54         6.58        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
       21.04         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       40.08        28.41        32.94        29.98        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        21.11        12.43        10.62         0.79 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.00 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             79.07             122.30 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             9.485             13.350 
[1] "0.1 - 79.1 (9.5)"   "0.0 - 122.3 (13.3)"
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0        1        4        5         9        12
  12Q GAIN WILD-TYPE       3       13       37       26        29        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           2         18         12          4        9
  12Q GAIN WILD-TYPE         2         67         50         37       37
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  1                 13
  STAGE IB                  4                 37
  STAGE II                  5                 26
  STAGE IIA                 9                 29
  STAGE IIB                12                 43
  STAGE III                 2                  2
  STAGE IIIA               18                 67
  STAGE IIIB               12                 50
  STAGE IIIC                4                 37
  STAGE IV                  9                 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
  12Q GAIN MUTATED     3  11  43  19
  12Q GAIN WILD-TYPE  19  79 152 100
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                3                 19
  T2               11                 79
  T3               43                152
  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    18  21  24  12
  12Q GAIN WILD-TYPE 111  97  60  77
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               18                111
  N1               21                 97
  N2               24                 60
  N3               12                 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"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    67   6
  12Q GAIN WILD-TYPE 320  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     67    6
  12Q GAIN WILD-TYPE  320   24
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               67                320
  1                6                 24
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    25  51
  12Q GAIN WILD-TYPE 133 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     25   51
  12Q GAIN WILD-TYPE  133  227
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               25                133
  MALE                 51                227
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12Q GAIN MUTATED                                      17
  12Q GAIN WILD-TYPE                                    54
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                       22
  12Q GAIN WILD-TYPE                                                    140
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                                  11
  12Q GAIN WILD-TYPE                                                                70
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  12Q GAIN MUTATED                                                 19
  12Q GAIN WILD-TYPE                                               59
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12Q GAIN MUTATED                                                          3
  12Q GAIN WILD-TYPE                                                       18
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  12Q GAIN MUTATED                                                           2
  12Q GAIN WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12Q GAIN MUTATED                                          1
  12Q GAIN WILD-TYPE                                       12
D24V8, multiclass
                                                                   clus
vv                                                                  12Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  12Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 70
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          12
[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"
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  76
  12Q GAIN WILD-TYPE   6 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   76
  12Q GAIN WILD-TYPE    6  354
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 0                  6
  YES               76                354
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    60   3   4   2
  12Q GAIN WILD-TYPE 287  15  15  23
D24V10, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               60                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                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           0    41
  12Q GAIN WILD-TYPE                                         1   233
D24V12, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                                   23                 65
  BLACK OR AFRICAN AMERICAN                                1                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   41                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"
D24V13, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  57
  12Q GAIN WILD-TYPE   2 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   57
  12Q GAIN WILD-TYPE    2  256
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               57                256
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    94  48
  13Q GAIN WILD-TYPE 160 102
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               142                262 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                48                102 
$`13Q GAIN MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4279 TCGA-BR-4280 
       11.70        11.01         9.44         4.64         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6801 
       15.95        39.12         9.17        32.78        25.61        21.11 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8078 
        9.21        35.24        18.15        28.73         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8483 
        9.60        12.95        13.08        14.79        15.85         5.39 
TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        9.21        12.79        11.54        16.44        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       10.68        13.87        22.26         0.72        14.17        12.82 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QM 
       13.51         0.46        20.65        20.42         1.15         5.13 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8535 TCGA-CD-A48A 
        3.25        13.15         0.07         0.13         0.13        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 
        6.58        12.20        20.02        15.95         7.99        54.08 
TCGA-CG-4444 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5730 TCGA-CG-5732 
       47.05         7.07        12.00         1.02         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 
        7.99        12.36        12.66        19.13        18.54        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 
       17.19        10.26        15.98        10.55        11.31        19.50 
TCGA-D7-8574 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 
       17.19        14.27        14.76        11.24         2.96        15.65 
TCGA-D7-A747 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-A4BF 
        8.38         0.62         7.99        72.23        19.53         5.52 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GD 
       12.59        14.17        12.10        12.30        11.84        22.75 
TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
       25.81         6.51         6.25         0.26        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP 
       12.30        27.42        18.38         5.19         1.41         6.44 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        1.81         5.56        37.64         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 
        8.52         8.61       122.30        37.91       115.69        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
        8.94        35.61         5.79        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       13.02        21.73        34.45        22.19         2.70        17.85 
TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91Q 
       23.41        13.35        14.33        65.16        36.69        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R 
       22.68         1.71        36.16         9.04        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-VQ-AA6K 
       11.24        29.98        21.11        12.43 

$`13Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 
       26.70        19.56         9.47         6.61         6.97         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 
       18.35        30.90         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        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       23.93        15.42        28.01        15.32        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        12.76        18.71        17.49        14.43        11.44 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05         0.56         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         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-8384 TCGA-BR-8484 TCGA-BR-8486 
       11.80        19.17         0.26         3.72        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
        0.49        15.81         9.86        12.56         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 
        1.48        13.41        13.51        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        19.36        13.64        11.57         2.83        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.30         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        9.34        11.31        11.61         0.10        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       27.02         1.02         8.05         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       22.98        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-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       65.10        21.07        11.93        20.55        18.84        18.61 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       13.35        15.22        12.79        12.33        24.72        16.80 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       15.16        13.78        13.71        11.31        11.44         9.76 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 
        4.34         7.40         7.13        16.24        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        1.51         5.92        14.27        11.41        10.62         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        10.19         2.10        12.95 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39         5.36        13.08         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G 
        5.56         7.82        13.51         2.53        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        3.72        19.73        61.25         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        35.24        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       27.35        64.57        11.70        11.93        61.22        18.74 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 
        7.36         9.50         9.73        52.24         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94U 
        4.54         6.58         5.72        64.18         2.66        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        40.08        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        10.62         0.79 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.07               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            122.30             116.38 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            12.985             12.790 
[1] "0.1 - 122.3 (13.0)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.3"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         2        3        9       11        14        21
  13Q GAIN WILD-TYPE       1       11       32       20        24        34
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           1         33         20         12       20
  13Q GAIN WILD-TYPE         3         52         42         29       26
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   2                  1
  STAGE IA                  3                 11
  STAGE IB                  9                 32
  STAGE II                 11                 20
  STAGE IIA                14                 24
  STAGE IIB                21                 34
  STAGE III                 1                  3
  STAGE IIIA               33                 52
  STAGE IIIB               20                 42
  STAGE IIIC               12                 29
  STAGE IV                 20                 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
  13Q GAIN MUTATED     5  35  67  41
  13Q GAIN WILD-TYPE  17  55 128  78
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                5                 17
  T2               35                 55
  T3               67                128
  T4               41                 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"
                    vv
clus                 N0 N1 N2 N3
  13Q GAIN MUTATED   40 42 33 31
  13Q GAIN WILD-TYPE 89 76 51 58
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               40                 89
  N1               42                 76
  N2               33                 51
  N3               31                 58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   141  10
  13Q GAIN WILD-TYPE 246  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    141   10
  13Q GAIN WILD-TYPE  246   20
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0              141                246
  1               10                 20
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    48 105
  13Q GAIN WILD-TYPE 110 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     48  105
  13Q GAIN WILD-TYPE  110  173
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               48                110
  MALE                105                173
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  13Q GAIN MUTATED                                      17
  13Q GAIN WILD-TYPE                                    54
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                       55
  13Q GAIN WILD-TYPE                                                    107
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                                  31
  13Q GAIN WILD-TYPE                                                                50
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  13Q GAIN MUTATED                                                 30
  13Q GAIN WILD-TYPE                                               48
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  13Q GAIN MUTATED                                                         10
  13Q GAIN WILD-TYPE                                                       11
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  13Q GAIN MUTATED                                                           5
  13Q GAIN WILD-TYPE                                                         3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  13Q GAIN MUTATED                                          4
  13Q GAIN WILD-TYPE                                        9
D25V8, multiclass
                                                                   clus
vv                                                                  13Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          55
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         4
                                                                   clus
vv                                                                  13Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           107
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           9
[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"
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1 152
  13Q GAIN WILD-TYPE   5 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1  152
  13Q GAIN WILD-TYPE    5  278
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 1                  5
  YES              152                278
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED   119   8   6   9
  13Q GAIN WILD-TYPE 228  10  13  16
D25V10, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0              119                228
  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                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           1    93
  13Q GAIN WILD-TYPE                                         0   181
D25V12, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                                   31                 57
  BLACK OR AFRICAN AMERICAN                                6                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   93                181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1 111
  13Q GAIN WILD-TYPE   3 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1  111
  13Q GAIN WILD-TYPE    3  202
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO              111                202
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    13  15
  14Q GAIN WILD-TYPE 241 135
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                28                376 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                15                135 
$`14Q GAIN MUTATED`
TCGA-BR-4187 TCGA-BR-6705 TCGA-BR-8060 TCGA-BR-8295 TCGA-BR-A4J8 TCGA-BR-A4PE 
        4.64        25.61        11.44         2.20        13.51        20.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4444 TCGA-CG-4460 TCGA-D7-6518 TCGA-D7-A6F2 
        9.34        12.43        47.05        21.99        19.13        15.65 
TCGA-EQ-5647 TCGA-FP-A4BF TCGA-HU-8243 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A7NR 
        0.62         5.52         5.92        18.38         1.41         6.51 
TCGA-IN-A7NT TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-RD-A7BS TCGA-VQ-A8PE TCGA-VQ-A91V 
        5.56        45.67         8.52        11.05        22.19        36.16 
TCGA-VQ-A925 TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6I 
        4.54        42.54        40.08        16.14 

$`14Q GAIN WILD-TYPE`
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-4267 
        6.61         6.97         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        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-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        0.56        12.95         2.66        16.31        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        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 
       19.17        14.79         0.26        15.85         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        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        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        12.82         0.66        19.36         0.46        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         3.42        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         0.10        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-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
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-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        11.93        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-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO 
        8.38         4.34         7.40         7.13         7.99        16.24 
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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
        0.56         0.23        18.08        26.47         1.51        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.81        27.42        21.21         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19        13.08         6.44         6.74        12.59 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE 
       20.15        37.64         3.72        19.73         9.86        18.21 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW 
       61.25         6.08         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-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-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        28.96        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       20.81        22.68         1.71         7.36         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       52.24         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
       64.18        21.04         2.66        11.24        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        32.94        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         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 
             12.97              12.82 
[1] "0.6 - 47.0 (13.0)"  "0.0 - 122.3 (12.8)"
[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       2       13       39       31        37        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           0          7          4          3        6
  14Q GAIN WILD-TYPE         4         78         58         38       40
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  1                 13
  STAGE IB                  2                 39
  STAGE II                  0                 31
  STAGE IIA                 1                 37
  STAGE IIB                 3                 52
  STAGE III                 0                  4
  STAGE IIIA                7                 78
  STAGE IIIB                4                 58
  STAGE IIIC                3                 38
  STAGE IV                  6                 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
  14Q GAIN MUTATED     2   5  13   8
  14Q GAIN WILD-TYPE  20  85 182 111
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                2                 20
  T2                5                 85
  T3               13                182
  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   6   6  10
  14Q GAIN WILD-TYPE 123 112  78  79
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                6                123
  N1                6                112
  N2                6                 78
  N3               10                 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"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    24   5
  14Q GAIN WILD-TYPE 363  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     24    5
  14Q GAIN WILD-TYPE  363   25
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               24                363
  1                5                 25
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    12  17
  14Q GAIN WILD-TYPE 146 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     12   17
  14Q GAIN WILD-TYPE  146  261
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               12                146
  MALE                 17                261
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  14Q GAIN MUTATED                                       4
  14Q GAIN WILD-TYPE                                    67
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                       13
  14Q GAIN WILD-TYPE                                                    149
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                                   3
  14Q GAIN WILD-TYPE                                                                78
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  14Q GAIN MUTATED                                                  8
  14Q GAIN WILD-TYPE                                               70
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  14Q GAIN MUTATED                                                          0
  14Q GAIN WILD-TYPE                                                       21
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  14Q GAIN MUTATED                                                           0
  14Q GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  14Q GAIN MUTATED                                          1
  14Q GAIN WILD-TYPE                                       12
D26V8, multiclass
                                                                   clus
vv                                                                  14Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  14Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           149
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 78
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  70
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          12
[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"
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  29
  14Q GAIN WILD-TYPE   6 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   29
  14Q GAIN WILD-TYPE    6  401
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 0                  6
  YES               29                401
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    20   2   3   1
  14Q GAIN WILD-TYPE 327  16  16  24
D26V10, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               20                327
  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       4                         1
  14Q GAIN WILD-TYPE    84                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           0    21
  14Q GAIN WILD-TYPE                                         1   253
D26V12, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                                    4                 84
  BLACK OR AFRICAN AMERICAN                                1                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   21                253
[1] 4 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  20
  14Q GAIN WILD-TYPE   3 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   20
  14Q GAIN WILD-TYPE    3  293
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               20                293
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    17  20
  15Q GAIN WILD-TYPE 237 130
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                37                367 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                20                130 
$`15Q GAIN MUTATED`
TCGA-BR-4183 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7959 TCGA-BR-8683 TCGA-BR-8687 
        6.61        12.16         9.21        18.71         9.86         8.22 
TCGA-BR-A4J4 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-A486 TCGA-CG-4477 
        0.53         1.15         3.25         0.07         3.42        30.97 
TCGA-CG-5727 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6815 TCGA-EQ-5647 TCGA-F1-6875 
       79.07        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-IN-A6RO 
       11.38        17.06        11.77         3.45         3.39         1.41 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV 
       60.56        37.64        18.21         6.08         8.61       122.30 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       13.02        18.48        46.26        12.79         2.70        17.85 
TCGA-VQ-A925 
        4.54 

$`15Q GAIN WILD-TYPE`
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-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        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-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        32.94        12.82        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        12.76        17.49        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         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        19.50        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 
       19.17        14.79         0.26        15.85         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        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44        15.68        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
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        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       19.36        13.51         0.46        20.65        20.42        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       11.57         5.13         2.83        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        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 
        0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        22.98         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        12.36        12.66        11.93        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        10.55        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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        2.96        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        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-8631 
       14.07        22.29        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        5.52         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.81        27.42        21.21        18.81        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        5.19        13.08         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        5.56         1.81         7.82        13.51         2.53         5.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       20.15         3.72        19.73         9.86        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       61.25         4.60         9.24        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-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79         5.46        13.25        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       27.88        32.48         7.73        28.96        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       22.19         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       13.35        26.24        27.35        64.57        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       36.69        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       22.68         1.71        36.16         7.36         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       52.24         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
       64.18        21.04         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        40.08        28.41        32.94        29.98        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        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.07               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            122.30             116.38 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             11.77              12.95 
[1] "0.1 - 122.3 (11.8)" "0.0 - 116.4 (12.9)"
[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       3       11       39       28        35        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           2          9          7          2        5
  15Q GAIN WILD-TYPE         2         76         55         39       41
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  3                 11
  STAGE IB                  2                 39
  STAGE II                  3                 28
  STAGE IIA                 3                 35
  STAGE IIB                 3                 52
  STAGE III                 2                  2
  STAGE IIIA                9                 76
  STAGE IIIB                7                 55
  STAGE IIIC                2                 39
  STAGE IV                  5                 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
  15Q GAIN MUTATED     3   7  19  10
  15Q GAIN WILD-TYPE  19  83 176 109
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                3                 19
  T2                7                 83
  T3               19                176
  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 120 111  70  81
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                9                120
  N1                7                111
  N2               14                 70
  N3                8                 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"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    33   5
  15Q GAIN WILD-TYPE 354  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     33    5
  15Q GAIN WILD-TYPE  354   25
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               33                354
  1                5                 25
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    12  27
  15Q GAIN WILD-TYPE 146 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     12   27
  15Q GAIN WILD-TYPE  146  251
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               12                146
  MALE                 27                251
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  15Q GAIN MUTATED                                       4
  15Q GAIN WILD-TYPE                                    67
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                       12
  15Q GAIN WILD-TYPE                                                    150
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                                   9
  15Q GAIN WILD-TYPE                                                                72
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  15Q GAIN MUTATED                                                 10
  15Q GAIN WILD-TYPE                                               68
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  15Q GAIN MUTATED                                                          2
  15Q GAIN WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  15Q GAIN MUTATED                                                           0
  15Q GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  15Q GAIN MUTATED                                          2
  15Q GAIN WILD-TYPE                                       11
D27V8, multiclass
                                                                   clus
vv                                                                  15Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  15Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           150
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 72
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  68
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          11
[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"
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  39
  15Q GAIN WILD-TYPE   6 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   39
  15Q GAIN WILD-TYPE    6  391
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                  6
  YES               39                391
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    24   3   6   1
  15Q GAIN WILD-TYPE 323  15  13  24
D27V10, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               24                323
  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                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           1    19
  15Q GAIN WILD-TYPE                                         0   255
D27V12, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                                    9                 79
  BLACK OR AFRICAN AMERICAN                                4                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   19                255
[1] 4 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   4 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   26
  15Q GAIN WILD-TYPE    4  287
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               26                287
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    33  21
  16P GAIN WILD-TYPE 221 129
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                54                350 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                21                129 
$`16P GAIN MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-8080 
       11.01         9.44         4.64        17.29         9.17         9.60 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PD 
       25.18        20.22         7.53        12.82        13.51        20.65 
TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8529 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4460 
       13.18         0.10         0.13        54.08        47.05        21.99 
TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5730 
        0.00        12.00        22.98         1.02         0.99         4.01 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8576 TCGA-D7-A747 
       18.54        17.19        12.79        10.55        14.66         8.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX 
        3.48        14.07        22.29        17.06         0.56         0.23 
TCGA-HU-8249 TCGA-HU-A4GP TCGA-HU-A4GY TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RO 
       14.17         8.98         0.26         3.39         5.19         1.41 
TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-R5-A7ZE TCGA-RD-A7BT 
        6.44         5.56         1.81         2.53        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        29.98        54.12        16.14        12.43 

$`16P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        19.56         9.47         6.61         6.97 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         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-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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       12.26        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8487 
        0.26        15.85         3.72         5.39         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        10.68        12.56        13.87         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
       14.17         0.53         0.66        19.36         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        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         0.10        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-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97         6.97        36.00         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        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        12.36        12.66        11.93 
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-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       10.26        15.22        15.98        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       15.65         4.34         7.40         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
       16.24        14.47        72.23        21.27        11.38        19.53 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
       59.54         5.03        13.58         5.52        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        14.27        12.59        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
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         6.25        10.19         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
        8.81        27.42        21.21         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
        5.36        13.08         6.74        12.59         6.51         7.82 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
       13.51         5.56        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73         9.86        45.67         8.52        61.25         6.08 
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-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        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
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-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        36.16         7.36         9.50         9.73        52.24 
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        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
       21.04         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J 
       40.08        28.41        32.94        17.13        26.04        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.00               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             54.12             122.30 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             10.78              13.05 
[1] "0.0 - 54.1 (10.8)"  "0.1 - 122.3 (13.1)"
[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         9
  16P GAIN WILD-TYPE       3       12       39       31        35        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           0         20          4          7       10
  16P GAIN WILD-TYPE         4         65         58         34       36
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  2                 12
  STAGE IB                  2                 39
  STAGE II                  0                 31
  STAGE IIA                 3                 35
  STAGE IIB                 9                 46
  STAGE III                 0                  4
  STAGE IIIA               20                 65
  STAGE IIIB                4                 58
  STAGE IIIC                7                 34
  STAGE IV                 10                 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
  16P GAIN MUTATED     3  10  24  20
  16P GAIN WILD-TYPE  19  80 171  99
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                3                 19
  T2               10                 80
  T3               24                171
  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  13  14
  16P GAIN WILD-TYPE 118 101  71  75
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               11                118
  N1               17                101
  N2               13                 71
  N3               14                 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"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    45   6
  16P GAIN WILD-TYPE 342  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     45    6
  16P GAIN WILD-TYPE  342   24
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               45                342
  1                6                 24
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    20  39
  16P GAIN WILD-TYPE 138 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     20   39
  16P GAIN WILD-TYPE  138  239
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               20                138
  MALE                 39                239
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16P GAIN MUTATED                                       8
  16P GAIN WILD-TYPE                                    63
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                       25
  16P GAIN WILD-TYPE                                                    137
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                                  12
  16P GAIN WILD-TYPE                                                                69
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  16P GAIN MUTATED                                                  7
  16P GAIN WILD-TYPE                                               71
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16P GAIN MUTATED                                                          3
  16P GAIN WILD-TYPE                                                       18
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  16P GAIN MUTATED                                                           0
  16P GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16P GAIN MUTATED                                          2
  16P GAIN WILD-TYPE                                       11
D28V8, multiclass
                                                                   clus
vv                                                                  16P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  16P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  71
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          11
[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"
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     3  56
  16P GAIN WILD-TYPE   3 374
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3   56
  16P GAIN WILD-TYPE    3  374
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 3                  3
  YES               56                374
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    45   1   6   3
  16P GAIN WILD-TYPE 302  17  13  22
D28V10, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               45                302
  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                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           1    36
  16P GAIN WILD-TYPE                                         0   238
D28V12, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                                   11                 77
  BLACK OR AFRICAN AMERICAN                                1                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   36                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"
D28V13, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  42
  16P GAIN WILD-TYPE   3 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   42
  16P GAIN WILD-TYPE    3  271
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               42                271
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    23  19
  16Q GAIN WILD-TYPE 231 131
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                42                362 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                19                131 
$`16Q GAIN MUTATED`
TCGA-B7-A5TJ TCGA-BR-4187 TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J5 
       11.01         4.64        20.22         7.53         1.48        12.82 
TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8529 TCGA-CG-4438 TCGA-CG-4460 
       13.51        13.18         0.10         0.13        54.08        21.99 
TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-6521 
        0.00        12.00         1.02         0.99         4.01        18.54 
TCGA-D7-6818 TCGA-D7-8576 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       10.55        14.66         7.99         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8249 TCGA-IN-8663 TCGA-IN-A6RO 
       17.06         0.56         0.23        14.17         3.39         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-R5-A7ZE TCGA-RD-A7BT 
        6.44         6.74         5.56         1.81        18.21         8.61 
TCGA-VQ-A8DV TCGA-VQ-A8PS TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6K 
       13.25        13.35        29.98        54.12        16.14        12.43 

$`16Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        6.97         7.43        18.35        30.90         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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        12.95         2.66        16.31         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        19.50        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        19.17        14.79         0.26        15.85 
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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       10.68        12.56        13.87         6.08        22.26        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36         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 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        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         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
        7.07        22.98        30.97         6.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        6.02       105.07        12.03        15.02        28.96        79.07 
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        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        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-D7-6822 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 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         0.62        16.24        14.47        72.23 
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-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        5.52        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        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         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42        21.21         3.45        18.81        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
        5.19        13.08        12.59         6.51         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
        2.53         5.56        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73         9.86        45.67         8.52        61.25         6.08 
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-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-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.02        18.48        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.93        61.22        18.74        20.81        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       36.16         7.36         9.50         9.73        52.24         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        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
       21.04         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J 
       40.08        28.41        32.94        17.13        26.04        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.00               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             54.12             122.30 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            10.780             12.985 
[1] "0.0 - 54.1 (10.8)"  "0.1 - 122.3 (13.0)"
[1] "hr=" "1.8"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0        2        3        0         2         4
  16Q GAIN WILD-TYPE       3       12       38       31        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           0         14          3          7       10
  16Q GAIN WILD-TYPE         4         71         59         34       36
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  2                 12
  STAGE IB                  3                 38
  STAGE II                  0                 31
  STAGE IIA                 2                 36
  STAGE IIB                 4                 51
  STAGE III                 0                  4
  STAGE IIIA               14                 71
  STAGE IIIB                3                 59
  STAGE IIIC                7                 34
  STAGE IV                 10                 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
  16Q GAIN MUTATED     3   7  20  15
  16Q GAIN WILD-TYPE  19  83 175 104
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                3                 19
  T2                7                 83
  T3               20                175
  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  12   9  13
  16Q GAIN WILD-TYPE 119 106  75  76
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               10                119
  N1               12                106
  N2                9                 75
  N3               13                 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"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    33   6
  16Q GAIN WILD-TYPE 354  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     33    6
  16Q GAIN WILD-TYPE  354   24
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               33                354
  1                6                 24
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    15  32
  16Q GAIN WILD-TYPE 143 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     15   32
  16Q GAIN WILD-TYPE  143  246
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               15                143
  MALE                 32                246
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16Q GAIN MUTATED                                       5
  16Q GAIN WILD-TYPE                                    66
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                       19
  16Q GAIN WILD-TYPE                                                    143
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                                  14
  16Q GAIN WILD-TYPE                                                                67
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  16Q GAIN MUTATED                                                  4
  16Q GAIN WILD-TYPE                                               74
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16Q GAIN MUTATED                                                          2
  16Q GAIN WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  16Q GAIN MUTATED                                                           0
  16Q GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16Q GAIN MUTATED                                          2
  16Q GAIN WILD-TYPE                                       11
D29V8, multiclass
                                                                   clus
vv                                                                  16Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  16Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           143
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  74
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          11
[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"
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2  45
  16Q GAIN WILD-TYPE   4 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   45
  16Q GAIN WILD-TYPE    4  385
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 2                  4
  YES               45                385
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    34   1   5   3
  16Q GAIN WILD-TYPE 313  17  14  22
D29V10, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               34                313
  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       9                         1
  16Q GAIN WILD-TYPE    79                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           1    28
  16Q GAIN WILD-TYPE                                         0   246
D29V12, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                                    9                 79
  BLACK OR AFRICAN AMERICAN                                1                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   28                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"
D29V13, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  32
  16Q GAIN WILD-TYPE   3 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   32
  16Q GAIN WILD-TYPE    3  281
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               32                281
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    12  14
  17P GAIN WILD-TYPE 242 136
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                26                378 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                14                136 
$`17P GAIN MUTATED`
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8686 TCGA-BR-A4QI TCGA-CG-4455 TCGA-CG-4460 
       14.43        11.44        15.68        13.64        12.03        21.99 
TCGA-CG-4475 TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-6817 TCGA-D7-8573 TCGA-D7-A6EY 
       22.98         0.99        12.03        12.79        19.50        11.44 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7829 TCGA-HJ-7597 TCGA-HU-A4GF 
        0.62        16.24        72.23        19.53        26.47        25.81 
TCGA-HU-A4HD TCGA-R5-A7ZR TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 
       27.42         6.08        52.24         9.04         2.01         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R 
       21.04        42.54 

$`17P GAIN WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        12.95         2.66        16.31         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        19.50        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        19.17        14.79         0.26        15.85 
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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        0.49        11.54        15.81        16.44         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        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        12.82         0.66        19.36        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        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        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         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        47.05        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-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         6.02       105.07        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        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 
       12.36        12.66        11.93        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        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.24        11.31         9.76         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         7.40         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-A8CX 
       59.54         5.03        13.58         0.56         5.52         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       18.08         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
       12.30        11.84        24.20         3.25        22.75        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         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88         8.81        21.21         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         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        1.41         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       20.15        37.64         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52        61.25         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-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        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-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.93        61.22        18.74        20.81        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 
       36.16         7.36         9.50         9.73        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
        5.72        64.18         2.66        11.24        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       40.08        28.41        32.94        29.98        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        21.11        12.43        10.62         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 
            15.055             12.790 
[1] "0.6 - 72.2 (15.1)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         0        1        1        1         4         3
  17P GAIN WILD-TYPE       3       13       40       30        34        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           2          5          3          1        6
  17P GAIN WILD-TYPE         2         80         59         40       40
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  1                 13
  STAGE IB                  1                 40
  STAGE II                  1                 30
  STAGE IIA                 4                 34
  STAGE IIB                 3                 52
  STAGE III                 2                  2
  STAGE IIIA                5                 80
  STAGE IIIB                3                 59
  STAGE IIIC                1                 40
  STAGE IV                  6                 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
  17P GAIN MUTATED     0   5  15   8
  17P GAIN WILD-TYPE  22  85 180 111
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                0                 22
  T2                5                 85
  T3               15                180
  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
  17P GAIN MUTATED     6  10   5   5
  17P GAIN WILD-TYPE 123 108  79  84
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                6                123
  N1               10                108
  N2                5                 79
  N3                5                 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"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    21   4
  17P GAIN WILD-TYPE 366  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     21    4
  17P GAIN WILD-TYPE  366   26
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               21                366
  1                4                 26
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     9  19
  17P GAIN WILD-TYPE 149 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      9   19
  17P GAIN WILD-TYPE  149  259
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                9                149
  MALE                 19                259
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17P GAIN MUTATED                                       1
  17P GAIN WILD-TYPE                                    70
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                        7
  17P GAIN WILD-TYPE                                                    155
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                                   5
  17P GAIN WILD-TYPE                                                                76
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  17P GAIN MUTATED                                                 11
  17P GAIN WILD-TYPE                                               67
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17P GAIN MUTATED                                                          2
  17P GAIN WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  17P GAIN MUTATED                                                           0
  17P GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17P GAIN MUTATED                                          1
  17P GAIN WILD-TYPE                                       12
D30V8, multiclass
                                                                   clus
vv                                                                  17P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  17P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             70
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           155
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 76
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  67
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          12
[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"
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  27
  17P GAIN WILD-TYPE   5 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   27
  17P GAIN WILD-TYPE    5  403
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 1                  5
  YES               27                403
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    21   0   5   1
  17P GAIN WILD-TYPE 326  18  14  24
D30V10, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               21                326
  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                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0    16
  17P GAIN WILD-TYPE                                         1   258
D30V12, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                                    3                 85
  BLACK OR AFRICAN AMERICAN                                3                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   16                258
[1] 4 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   4 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   17
  17P GAIN WILD-TYPE    4  296
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               17                296
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    35  23
  17Q GAIN WILD-TYPE 219 127
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                58                346 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                23                127 
$`17Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
       11.70        14.43        11.44        12.95         2.66        15.58 
TCGA-BR-8369 TCGA-BR-8686 TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4QI 
       14.04        15.68        12.89         0.53        20.42        13.64 
TCGA-CD-A486 TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5719 
        3.42         7.99        12.03        21.99        22.98         1.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-8573 
        0.99        12.03        18.54        13.35        12.79        19.50 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7829 
       11.44         2.96         0.62        16.24        72.23        19.53 
TCGA-FP-7916 TCGA-HJ-7597 TCGA-HU-8604 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI 
       14.07        26.47        12.10        27.42        18.81        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        5.19         1.41         6.44         5.56         1.81         7.82 
TCGA-R5-A7ZR TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PZ TCGA-VQ-A91Q 
        6.08        13.25        13.02        18.48        65.16        20.81 
TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D 
       36.16        52.24         9.04         2.01         4.54        64.18 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6F 
       21.04        42.54        40.08        54.12 

$`17Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        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-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.56        16.31         2.20         7.40         6.18        19.50 
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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
       22.26         1.48        13.41        13.51         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65         1.15        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         9.34        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         0.10        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-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        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-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 
        6.97        36.00         0.99         6.02       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        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        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.61        17.85        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        10.55        11.31        12.33        24.72        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-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.24        11.31         9.76        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.40         7.13         7.99        14.47        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
        0.56         5.52         0.23        18.08         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
       14.27        12.59        14.17        11.41        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
        8.81        21.21         3.45         3.39         5.36        13.08 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.74        12.59         6.51        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
       60.56        20.15        37.64         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52        61.25         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-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        28.96        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-A8PU TCGA-VQ-A8PX 
       23.41        15.65        13.35        26.24        27.35        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       14.33        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 
       22.68         1.71         7.36         9.50         9.73        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
        6.58         5.72         2.66        11.24        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        32.94        29.98        17.13        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.53               0.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             72.23             122.30 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             13.30              12.71 
[1] "0.5 - 72.2 (13.3)"  "0.0 - 122.3 (12.7)"
[1] "hr=" "1"  
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         1        3        7        3         5         6
  17Q GAIN WILD-TYPE       2       11       34       28        33        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           2         11          5          6       10
  17Q GAIN WILD-TYPE         2         74         57         35       36
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  3                 11
  STAGE IB                  7                 34
  STAGE II                  3                 28
  STAGE IIA                 5                 33
  STAGE IIB                 6                 49
  STAGE III                 2                  2
  STAGE IIIA               11                 74
  STAGE IIIB                5                 57
  STAGE IIIC                6                 35
  STAGE IV                 10                 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
  17Q GAIN MUTATED     4  15  25  16
  17Q GAIN WILD-TYPE  18  75 170 103
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                4                 18
  T2               15                 75
  T3               25                170
  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
  17Q GAIN MUTATED    20  14  11  13
  17Q GAIN WILD-TYPE 109 104  73  76
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               20                109
  N1               14                104
  N2               11                 73
  N3               13                 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"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    49   7
  17Q GAIN WILD-TYPE 338  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     49    7
  17Q GAIN WILD-TYPE  338   23
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               49                338
  1                7                 23
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    18  42
  17Q GAIN WILD-TYPE 140 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     18   42
  17Q GAIN WILD-TYPE  140  236
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               18                140
  MALE                 42                236
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17Q GAIN MUTATED                                       5
  17Q GAIN WILD-TYPE                                    66
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                       21
  17Q GAIN WILD-TYPE                                                    141
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                                  13
  17Q GAIN WILD-TYPE                                                                68
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  17Q GAIN MUTATED                                                 15
  17Q GAIN WILD-TYPE                                               63
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17Q GAIN MUTATED                                                          2
  17Q GAIN WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  17Q GAIN MUTATED                                                           0
  17Q GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17Q GAIN MUTATED                                          3
  17Q GAIN WILD-TYPE                                       10
D31V8, multiclass
                                                                   clus
vv                                                                  17Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  17Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  63
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          10
[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"
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1  59
  17Q GAIN WILD-TYPE   5 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   59
  17Q GAIN WILD-TYPE    5  371
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 1                  5
  YES               59                371
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    50   0   6   1
  17Q GAIN WILD-TYPE 297  18  13  24
D31V10, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               50                297
  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       8                         5
  17Q GAIN WILD-TYPE    80                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    37
  17Q GAIN WILD-TYPE                                         1   237
D31V12, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                                    8                 80
  BLACK OR AFRICAN AMERICAN                                5                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   37                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"
D31V13, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  38
  17Q GAIN WILD-TYPE   4 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   38
  17Q GAIN WILD-TYPE    4  275
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               38                275
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    40  34
  18P GAIN WILD-TYPE 214 116
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                74                330 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                34                116 
$`18P GAIN MUTATED`
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6565 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-8060 
        6.97        18.35         9.17        15.32         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.69         9.60         8.05         2.20        15.58         7.40 
TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8687 
       13.08         3.32         9.21        20.22         1.12         8.22 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 
        0.72        13.51        20.65         1.15         2.83         3.25 
TCGA-CD-5800 TCGA-CD-A486 TCGA-CD-A4MH TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5724 
       13.15         3.42        12.20        21.99        22.98        12.03 
TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8576 
       11.93        17.19        10.26        15.22        12.79        14.66 
TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-FP-8631 
       13.78        11.31         2.96        15.65         7.40         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.52        26.47         5.92         0.76        22.75        25.81 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       12.30        27.42        18.38        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A663 TCGA-R5-A7ZI TCGA-RD-A8N9 
        6.74         5.56        60.56         9.86        61.25        35.61 
TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
        0.92        21.73        22.19         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A922 TCGA-VQ-AA68 
        9.27        11.93        18.74         1.71         9.04        40.08 
TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       32.94         0.79 

$`18P GAIN WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        6.61         4.64         7.43        30.90         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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       15.42        28.01        18.15        28.73        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 
       12.76        18.71        17.49        14.43        12.26        20.55 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 
        0.56        12.95         2.66        16.31         6.18        19.50 
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-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72         5.39        25.18        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36         0.46        20.42        13.64        11.57         5.13 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.13         0.10         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        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-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       69.04        21.07         7.99        12.36        12.66        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-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        10.55        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-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        15.16        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       11.44         9.76         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.99        16.24        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-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 
        5.03        13.58         0.23        18.08         1.51        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
       12.59        14.17        11.41        12.10        10.62        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH 
        5.59        12.30        11.84        24.20         3.25        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         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
        3.39         5.36         5.19        12.59         6.51         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H 
        7.82        13.51         2.53         5.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
        3.72        19.73        45.67        18.21         8.52         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-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT 
       57.44         8.94        16.87        19.04         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        5.46        13.25        13.02        18.48        35.24        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       16.31         2.50        12.79        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       11.70        61.22        20.81        22.68        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50         9.73        52.24         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        64.18        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       11.24        22.09        18.41        28.41        29.98        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        21.11        12.43        10.62 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.56               0.00 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             61.25             122.30 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            11.375             13.300 
[1] "0.6 - 61.2 (11.4)"  "0.0 - 122.3 (13.3)"
[1] "hr=" "1.7"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         1        3        7        5         7         9
  18P GAIN WILD-TYPE       2       11       34       26        31        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           0         15          9         14        9
  18P GAIN WILD-TYPE         4         70         53         27       37
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  3                 11
  STAGE IB                  7                 34
  STAGE II                  5                 26
  STAGE IIA                 7                 31
  STAGE IIB                 9                 46
  STAGE III                 0                  4
  STAGE IIIA               15                 70
  STAGE IIIB                9                 53
  STAGE IIIC               14                 27
  STAGE IV                  9                 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
  18P GAIN MUTATED     7  12  33  27
  18P GAIN WILD-TYPE  15  78 162  92
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                7                 15
  T2               12                 78
  T3               33                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    24  20  13  23
  18P GAIN WILD-TYPE 105  98  71  66
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               24                105
  N1               20                 98
  N2               13                 71
  N3               23                 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"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    72   5
  18P GAIN WILD-TYPE 315  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     72    5
  18P GAIN WILD-TYPE  315   25
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               72                315
  1                5                 25
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    36  46
  18P GAIN WILD-TYPE 122 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     36   46
  18P GAIN WILD-TYPE  122  232
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               36                122
  MALE                 46                232
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18P GAIN MUTATED                                       7
  18P GAIN WILD-TYPE                                    64
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                       32
  18P GAIN WILD-TYPE                                                    130
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                                  12
  18P GAIN WILD-TYPE                                                                69
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  18P GAIN MUTATED                                                 19
  18P GAIN WILD-TYPE                                               59
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18P GAIN MUTATED                                                          4
  18P GAIN WILD-TYPE                                                       17
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  18P GAIN MUTATED                                                           3
  18P GAIN WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18P GAIN MUTATED                                          4
  18P GAIN WILD-TYPE                                        9
D32V8, multiclass
                                                                   clus
vv                                                                  18P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         4
                                                                   clus
vv                                                                  18P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           9
[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"
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4  78
  18P GAIN WILD-TYPE   2 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4   78
  18P GAIN WILD-TYPE    2  352
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 4                  2
  YES               78                352
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    65   5   4   4
  18P GAIN WILD-TYPE 282  13  15  21
D32V10, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               65                282
  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"
D32V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED      16                         0
  18P GAIN WILD-TYPE    72                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           0    54
  18P GAIN WILD-TYPE                                         1   220
D32V12, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                                   16                 72
  BLACK OR AFRICAN AMERICAN                                0                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   54                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  59
  18P GAIN WILD-TYPE   3 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   59
  18P GAIN WILD-TYPE    3  254
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               59                254
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    26  20
  18Q GAIN WILD-TYPE 228 130
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                46                358 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                20                130 
$`18Q GAIN MUTATED`
TCGA-BR-4184 TCGA-BR-6565 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
        6.97         9.17         3.45         0.69         9.60         8.05 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8484 TCGA-BR-8487 
        2.20        15.58         7.40        13.08        25.18         1.12 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5798 
        1.48         0.72        13.51        20.65         1.15         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CG-4460 TCGA-D7-5579 TCGA-D7-6528 TCGA-D7-6817 
        3.25        13.15        21.99        11.93        15.22        12.79 
TCGA-D7-A4YY TCGA-D7-A6EX TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.78        11.31         0.56         5.52        26.47         5.92 
TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI 
        0.76        22.75        25.81        12.30        27.42        18.38 
TCGA-IN-A6RN TCGA-R5-A7ZI TCGA-RD-A8N9 TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       13.08        61.25        35.61         2.70         1.87         9.27 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       11.93        18.74        40.08         0.79 

$`18Q GAIN WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.61         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12        26.10        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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       11.44        12.26        20.55         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       16.31         6.18        19.50         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 
       19.17        14.79         0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        22.26        13.41        13.51        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        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 
        0.46        20.42        13.64        11.57         5.13        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        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         0.10        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-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        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-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.36        12.66        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-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        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-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        15.16        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        7.40         7.13         0.62         7.99        16.24        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-A8CX 
       22.29        17.06        59.54         5.03        13.58         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       18.08         1.51        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10        10.62        24.30         5.59        12.30        11.84 
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-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        23.84         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21         3.45        18.81         3.39         5.36         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        1.41         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       20.15        37.64         3.72        19.73         9.86        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-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-A8NB 
      115.69       116.38        71.38        57.44         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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       22.19         2.50        12.79        17.85        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       13.35        26.24        27.35        64.57        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       36.69        11.70        61.22        20.81        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       36.16         7.36         9.50         9.73        52.24         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        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
       21.04         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        32.94        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        21.11        12.43        10.62 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.56               0.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             61.25             122.30 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            11.620             12.985 
[1] "0.6 - 61.2 (11.6)"  "0.0 - 122.3 (13.0)"
[1] "hr=" "1.5"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         1        1        4        4         2         6
  18Q GAIN WILD-TYPE       2       13       37       27        36        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           0         10          5         11        7
  18Q GAIN WILD-TYPE         4         75         57         30       39
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  1                 13
  STAGE IB                  4                 37
  STAGE II                  4                 27
  STAGE IIA                 2                 36
  STAGE IIB                 6                 49
  STAGE III                 0                  4
  STAGE IIIA               10                 75
  STAGE IIIB                5                 57
  STAGE IIIC               11                 30
  STAGE IV                  7                 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
  18Q GAIN MUTATED     3   8  15  25
  18Q GAIN WILD-TYPE  19  82 180  94
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                3                 19
  T2                8                 82
  T3               15                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    15  11   9  16
  18Q GAIN WILD-TYPE 114 107  75  73
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               15                114
  N1               11                107
  N2                9                 75
  N3               16                 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    44   4
  18Q GAIN WILD-TYPE 343  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     44    4
  18Q GAIN WILD-TYPE  343   26
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               44                343
  1                4                 26
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    24  29
  18Q GAIN WILD-TYPE 134 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     24   29
  18Q GAIN WILD-TYPE  134  249
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               24                134
  MALE                 29                249
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18Q GAIN MUTATED                                       5
  18Q GAIN WILD-TYPE                                    66
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                       20
  18Q GAIN WILD-TYPE                                                    142
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                                   6
  18Q GAIN WILD-TYPE                                                                75
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  18Q GAIN MUTATED                                                 12
  18Q GAIN WILD-TYPE                                               66
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18Q GAIN MUTATED                                                          4
  18Q GAIN WILD-TYPE                                                       17
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  18Q GAIN MUTATED                                                           2
  18Q GAIN WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18Q GAIN MUTATED                                          4
  18Q GAIN WILD-TYPE                                        9
D33V8, multiclass
                                                                   clus
vv                                                                  18Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         4
                                                                   clus
vv                                                                  18Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           142
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 75
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  66
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           9
[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"
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     3  50
  18Q GAIN WILD-TYPE   3 380
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3   50
  18Q GAIN WILD-TYPE    3  380
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 3                  3
  YES               50                380
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    42   3   3   3
  18Q GAIN WILD-TYPE 305  15  16  22
D33V10, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               42                305
  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      12                         0
  18Q GAIN WILD-TYPE    76                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           0    34
  18Q GAIN WILD-TYPE                                         1   240
D33V12, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                                   12                 76
  BLACK OR AFRICAN AMERICAN                                0                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   34                240
[1] 4 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  41
  18Q GAIN WILD-TYPE   3 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   41
  18Q GAIN WILD-TYPE    3  272
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               41                272
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    33  12
  19P GAIN WILD-TYPE 221 138
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                45                359 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                12                138 
$`19P GAIN MUTATED`
TCGA-B7-A5TK TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8291 
        9.47        17.29        19.33        18.71        12.95        16.31 
TCGA-BR-8370 TCGA-BR-A453 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8526 
        3.32         6.08        13.51        13.64        13.18         0.07 
TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48C TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
        0.16         0.13        11.61        47.05        19.07        21.99 
TCGA-CG-4475 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 
       22.98         0.99         4.01        12.36        19.13        20.55 
TCGA-D7-6521 TCGA-D7-6528 TCGA-D7-8578 TCGA-D7-A4YU TCGA-EQ-A4SO TCGA-FP-A4BF 
       18.54        15.22        21.14        16.44        16.24         5.52 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4H2 TCGA-IN-7808 
       14.17        12.10        24.30        22.75        12.95         3.45 
TCGA-IN-A6RP TCGA-SW-A7EB TCGA-VQ-A8E3 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A91A 
        6.44         5.79        21.73        22.19        12.79        36.69 
TCGA-VQ-A91S TCGA-VQ-A925 TCGA-VQ-A92D 
       22.68         4.54        64.18 

$`19P GAIN WILD-TYPE`
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-4267 
        6.97         4.64         7.43        18.35        30.90         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-6803 
       19.89        12.16         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        12.76        17.49        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66         2.20        15.58         7.40         6.18        19.50 
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-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        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        12.82         0.66        19.36 
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        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        2.83         3.25        13.15         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.13         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        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         0.10        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-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10        69.04        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       12.66        11.93        18.84        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.98        12.79        10.55        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-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        2.96        15.65         8.38         4.34         7.40         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-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
        1.51         5.92        14.27        12.59        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         5.59        12.30        11.84        24.20         3.25 
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-A4H3 
        6.51         6.25        10.19         0.26         2.10        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        12.30         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21        18.81         3.39        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         1.41         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       20.15        37.64         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        61.25         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-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        16.87        19.04         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        18.48        35.24        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       65.16        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        36.16         7.36         9.50         9.73        52.24 
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-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
        2.66        42.54        11.24        22.09        18.41        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        32.94        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.07               0.00 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             64.18             122.30 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             14.17              12.62 
[1] "0.1 - 64.2 (14.2)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1.4"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         0        0        4        3         3         7
  19P GAIN WILD-TYPE       3       14       37       28        35        48
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           1         14         10          2        6
  19P GAIN WILD-TYPE         3         71         52         39       40
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  0                 14
  STAGE IB                  4                 37
  STAGE II                  3                 28
  STAGE IIA                 3                 35
  STAGE IIB                 7                 48
  STAGE III                 1                  3
  STAGE IIIA               14                 71
  STAGE IIIB               10                 52
  STAGE IIIC                2                 39
  STAGE IV                  6                 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
  19P GAIN MUTATED     1  13  29   8
  19P GAIN WILD-TYPE  21  77 166 111
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                1                 21
  T2               13                 77
  T3               29                166
  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  20   8  14
  19P GAIN WILD-TYPE 120  98  76  75
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                9                120
  N1               20                 98
  N2                8                 76
  N3               14                 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"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    45   6
  19P GAIN WILD-TYPE 342  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     45    6
  19P GAIN WILD-TYPE  342   24
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               45                342
  1                6                 24
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    20  33
  19P GAIN WILD-TYPE 138 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     20   33
  19P GAIN WILD-TYPE  138  245
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               20                138
  MALE                 33                245
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19P GAIN MUTATED                                      11
  19P GAIN WILD-TYPE                                    60
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                       17
  19P GAIN WILD-TYPE                                                    145
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                                   5
  19P GAIN WILD-TYPE                                                                76
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  19P GAIN MUTATED                                                 12
  19P GAIN WILD-TYPE                                               66
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19P GAIN MUTATED                                                          5
  19P GAIN WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  19P GAIN MUTATED                                                           0
  19P GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19P GAIN MUTATED                                          2
  19P GAIN WILD-TYPE                                       11
D34V8, multiclass
                                                                   clus
vv                                                                  19P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  19P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           145
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 76
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  66
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          11
[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"
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     2  51
  19P GAIN WILD-TYPE   4 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   51
  19P GAIN WILD-TYPE    4  379
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 2                  4
  YES               51                379
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    37   4   5   4
  19P GAIN WILD-TYPE 310  14  14  21
D34V10, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               37                310
  R1                4                 14
  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"
D34V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED      11                         1
  19P GAIN WILD-TYPE    77                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           0    32
  19P GAIN WILD-TYPE                                         1   242
D34V12, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                                   11                 77
  BLACK OR AFRICAN AMERICAN                                1                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   32                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"
D34V13, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  37
  19P GAIN WILD-TYPE   4 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   37
  19P GAIN WILD-TYPE    4  276
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               37                276
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    44  23
  19Q GAIN WILD-TYPE 210 127
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                67                337 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                127 
$`19Q GAIN MUTATED`
TCGA-B7-A5TK TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8291 
        9.47        19.33        28.01        18.71        12.95        16.31 
TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8690 TCGA-BR-A453 TCGA-BR-A4J1 
        3.32         9.21         1.12        10.68         6.08         0.72 
TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 
       13.51        13.18         0.07         0.07         0.16         0.13 
TCGA-CD-A48C TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5722 
       11.61        54.08        47.05        21.99        22.98         0.99 
TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6818 TCGA-D7-6822 
        4.01        12.36        19.13        18.54        10.55        12.33 
TCGA-D7-8570 TCGA-D7-8578 TCGA-D7-A4YU TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       24.72        21.14        16.44         7.99        16.24        72.23 
TCGA-FP-7916 TCGA-FP-A4BF TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 
       14.07         5.52        14.27        14.17        12.10        24.30 
TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RP 
       22.75         2.10        12.95         3.45         5.19         6.44 
TCGA-KB-A6F7 TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DV 
       60.56         6.08         8.61        35.61         5.79        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A91A TCGA-VQ-A91S 
       21.73         7.73        22.19        12.79        36.69        22.68 
TCGA-VQ-A91U TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA6F 
        1.71         2.01         4.54        64.18        11.24        54.12 
TCGA-VQ-AA6K 
       12.43 

$`19Q GAIN WILD-TYPE`
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-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        15.42        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        12.76        17.49        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66         2.20        15.58         7.40         6.18        19.50 
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-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 
       15.85         3.72         5.39        25.18        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         7.53        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         8.98        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36         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 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43         6.58        12.20         0.10        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-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05         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-5723 
        6.97        36.00         1.02         0.99         6.02       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
       12.03        15.02        28.96        79.07        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        12.66        11.93        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-D7-6820 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       15.98        12.79        11.31        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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
        9.76         2.96        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.13         0.62        14.47        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        0.56         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.59        11.41        10.62         0.76         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        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         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        8.81        27.42        21.21        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        5.36        13.08         1.41         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        5.56         1.81         7.82        13.51         2.53         5.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       20.15        37.64         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52        61.25         4.60         9.24        11.05 
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-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.02        18.48        35.24 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       34.45        27.88        32.48        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       16.31         2.50         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
       23.41        15.65        13.35        26.24        27.35        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       14.33        65.16        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81        36.16         7.36         9.50         9.73        52.24 
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-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        22.09        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       29.98        17.13        26.04        16.14        21.11        10.62 
TCGA-ZQ-A9CR 
        0.79 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.07               0.00 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             72.23             122.30 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             12.79              12.82 
[1] "0.1 - 72.2 (12.8)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         0        2        6        4         4         9
  19Q GAIN WILD-TYPE       3       12       35       27        34        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           2         20         12          6        8
  19Q GAIN WILD-TYPE         2         65         50         35       38
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  2                 12
  STAGE IB                  6                 35
  STAGE II                  4                 27
  STAGE IIA                 4                 34
  STAGE IIB                 9                 46
  STAGE III                 2                  2
  STAGE IIIA               20                 65
  STAGE IIIB               12                 50
  STAGE IIIC                6                 35
  STAGE IV                  8                 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
  19Q GAIN MUTATED     3  16  41  14
  19Q GAIN WILD-TYPE  19  74 154 105
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                3                 19
  T2               16                 74
  T3               41                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  22
  19Q GAIN WILD-TYPE 115  91  74  67
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               14                115
  N1               27                 91
  N2               10                 74
  N3               22                 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"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    66   6
  19Q GAIN WILD-TYPE 321  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     66    6
  19Q GAIN WILD-TYPE  321   24
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               66                321
  1                6                 24
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    26  50
  19Q GAIN WILD-TYPE 132 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     26   50
  19Q GAIN WILD-TYPE  132  228
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               26                132
  MALE                 50                228
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19Q GAIN MUTATED                                      15
  19Q GAIN WILD-TYPE                                    56
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                       23
  19Q GAIN WILD-TYPE                                                    139
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                                  14
  19Q GAIN WILD-TYPE                                                                67
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  19Q GAIN MUTATED                                                 16
  19Q GAIN WILD-TYPE                                               62
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19Q GAIN MUTATED                                                          4
  19Q GAIN WILD-TYPE                                                       17
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  19Q GAIN MUTATED                                                           0
  19Q GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19Q GAIN MUTATED                                          3
  19Q GAIN WILD-TYPE                                       10
D35V8, multiclass
                                                                   clus
vv                                                                  19Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  19Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  62
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          10
[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"
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     4  72
  19Q GAIN WILD-TYPE   2 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      4   72
  19Q GAIN WILD-TYPE    2  358
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 4                  2
  YES               72                358
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    54   6   6   4
  19Q GAIN WILD-TYPE 293  12  13  21
D35V10, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               54                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                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           1    42
  19Q GAIN WILD-TYPE                                         0   232
D35V12, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                                   18                 70
  BLACK OR AFRICAN AMERICAN                                3                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   42                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"
D35V13, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0  51
  19Q GAIN WILD-TYPE   4 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   51
  19Q GAIN WILD-TYPE    4  262
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               51                262
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   142  85
  20P GAIN WILD-TYPE 112  65
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               227                177 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                85                 65 
$`20P GAIN MUTATED`
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-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
       18.35        30.90         6.61        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 
       19.33        39.12         9.17        18.05        19.89        21.11 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
       12.82         9.21        35.24        15.42        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 
       28.73         3.45        12.76        18.71        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        9.60         0.56        16.31         2.20        15.58         7.40 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.04        14.79         0.26         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       20.22        15.81         9.34         7.53         0.49        11.54 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 
        9.86        15.68         8.22        10.68        13.87         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4J9 
       22.26         1.48         0.72         0.53        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       20.42         1.15        13.64         3.25        13.15        13.18 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.13         0.13         3.42         9.34 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20         0.10        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         7.99        54.08         4.01        14.01 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       47.05        12.03        18.97         7.07        12.00        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
       36.00         1.02         0.99        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
        4.01         7.99        12.36        12.66        11.93        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        10.55 
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        15.16        13.71        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-8122 
        9.76         2.96        15.65         8.38         7.40         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-A8CX TCGA-HJ-7597 TCGA-HU-8238 
       17.06         0.56         5.52         0.23        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        14.27        12.59        10.62         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       12.30         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         6.25        10.19         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         9.67        27.42        21.21         3.45        18.38 
TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        5.19         6.74        12.59         5.56         1.81        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZE 
        5.56        60.56        20.15        37.64         9.86        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 
        8.52        61.25         6.08         9.24         8.61        16.67 
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        35.24        21.73        46.26        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A8PU TCGA-VQ-A8PX 
       12.79         2.70        17.85        15.65        27.35        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       65.16        36.69        11.93        18.74        22.68         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A928 
        7.36         9.73        52.24         9.04         2.01         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A 
       64.18        21.04        42.54        11.24        18.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        26.04        12.43        10.62         0.79 

$`20P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4267 TCGA-BR-4279 
       26.70        11.70        19.56         7.43         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 
       34.68        17.29        26.10        32.78        25.61        12.16 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 
        8.98        30.90        31.20        32.94        24.76        23.93 
TCGA-BR-7716 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
       28.01        12.43         9.07        17.49        14.43        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8360 TCGA-BR-8361 
       20.55         8.05        12.95         2.66         6.18        19.50 
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        19.17        15.85         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-8682 
        1.12        12.79        13.45         6.28        15.81        16.44 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       12.56         6.08        13.41        13.51        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4QL 
       14.17        12.82         0.66        19.36        20.65        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8531 TCGA-CD-8536 
        5.13         2.83         0.30         0.07         0.10         0.10 
TCGA-CD-A489 TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 
       11.31        12.62         3.02         1.02         8.05        29.98 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4475 TCGA-CG-5717 
       19.07        21.99         0.00         9.01        22.98         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-EQ-A4SO TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       16.24        21.27         3.48        59.54         5.03        13.58 
TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4G3 TCGA-HU-A4G8 
       18.08        14.17        11.41        12.10         5.59        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H5 
       24.20        21.37        29.98         6.51        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
        8.88         8.81        18.81         3.39         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IP-7968 TCGA-MX-A5UG 
        1.41         6.44         6.51         7.82         2.53         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
       19.73        45.67         4.60        11.05         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA 
       37.91        40.64       116.38        71.38        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        0.92        48.79         5.46        18.48        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PM 
       32.48         7.73        28.96        34.29        16.31         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91D 
        9.27        23.41        13.35        26.24        14.33        11.70 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A925 
       61.22        20.81        36.16         9.50        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D 
        6.58         2.66        22.09        40.08        28.41        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       54.12        16.14        21.11 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.00 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            115.69             122.30 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             12.30              13.78 
[1] "0.1 - 115.7 (12.3)" "0.0 - 122.3 (13.8)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         2        9       19       16        21        28
  20P GAIN WILD-TYPE       1        5       22       15        17        27
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           3         54         34         23       21
  20P GAIN WILD-TYPE         1         31         28         18       25
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   2                  1
  STAGE IA                  9                  5
  STAGE IB                 19                 22
  STAGE II                 16                 15
  STAGE IIA                21                 17
  STAGE IIB                28                 27
  STAGE III                 3                  1
  STAGE IIIA               54                 31
  STAGE IIIB               34                 28
  STAGE IIIC               23                 18
  STAGE IV                 21                 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
  20P GAIN MUTATED    11  48 115  60
  20P GAIN WILD-TYPE  11  42  80  59
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               11                 11
  T2               48                 42
  T3              115                 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   64 73 45 47
  20P GAIN WILD-TYPE 65 45 39 42
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               64                 65
  N1               73                 45
  N2               45                 39
  N3               47                 42
[1] 4 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   216  13
  20P GAIN WILD-TYPE 171  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    216   13
  20P GAIN WILD-TYPE  171   17
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              216                171
  1               13                 17
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    76 164
  20P GAIN WILD-TYPE  82 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     76  164
  20P GAIN WILD-TYPE   82  114
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               76                 82
  MALE                164                114
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  20P GAIN MUTATED                                      30
  20P GAIN WILD-TYPE                                    41
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                       84
  20P GAIN WILD-TYPE                                                     78
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                                  52
  20P GAIN WILD-TYPE                                                                29
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  20P GAIN MUTATED                                                 50
  20P GAIN WILD-TYPE                                               28
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  20P GAIN MUTATED                                                         10
  20P GAIN WILD-TYPE                                                       11
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  20P GAIN MUTATED                                                           5
  20P GAIN WILD-TYPE                                                         3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  20P GAIN MUTATED                                          8
  20P GAIN WILD-TYPE                                        5
D36V8, multiclass
                                                                   clus
vv                                                                  20P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           30
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          84
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         8
                                                                   clus
vv                                                                  20P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             41
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            78
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           5
[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"
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2 238
  20P GAIN WILD-TYPE   4 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  238
  20P GAIN WILD-TYPE    4  192
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 2                  4
  YES              238                192
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED   191   9   9  14
  20P GAIN WILD-TYPE 156   9  10  11
D36V10, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              191                156
  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                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           1   148
  20P GAIN WILD-TYPE                                         0   126
D36V12, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                                   53                 35
  BLACK OR AFRICAN AMERICAN                                6                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  148                126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2 176
  20P GAIN WILD-TYPE   2 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  176
  20P GAIN WILD-TYPE    2  137
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO              176                137
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   162  98
  20Q GAIN WILD-TYPE  92  52
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               260                144 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                98                 52 
$`20Q GAIN MUTATED`
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-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       18.35        30.90         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6706 
       13.68        19.33        39.12        26.10         9.17        18.05 
TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       19.89        21.11        12.82         9.21        35.24        15.42 
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        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8289 
       14.43        11.44         0.69         9.60         0.56         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8373 
       16.31         2.20        15.58         7.40        14.04        14.79 
TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 
        0.26         5.39        25.18         9.21        20.22        15.81 
TCGA-BR-8590 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        9.34         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       15.68         8.22        10.68        13.87         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4J9 
        1.48        12.89         0.72         0.53        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 
       20.65        20.42         1.15        13.64         3.25        13.15 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       13.18         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.13         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        12.43        11.61         6.58        12.20         0.10 
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-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 
        4.01        14.01        47.05        12.03        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 
       12.00        22.98        30.97        36.00         1.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        28.96        79.07         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.54        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
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-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       15.16        13.71        11.24        11.31         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.65         8.38         7.40         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 
       17.06         0.56         5.52         0.23        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        0.76        24.30        12.30         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        2.10        12.95        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR 
       21.21         3.45         3.39        18.38         5.19         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         5.56         1.81        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       60.56        20.15        37.64         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW 
        8.52        61.25         6.08         8.61        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU 
      115.69        57.44         8.94        35.61         5.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC 
       13.25        13.02        18.48        35.24        21.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PQ 
       22.19         2.50        12.79         2.70        17.85        15.65 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E 
       27.35        64.57        14.33        65.16        36.69        11.93 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A928 
        9.73        52.24         9.04         2.01         4.54         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       64.18        21.04        42.54        11.24        18.41        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        29.98        54.12        26.04        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

$`20Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4267 TCGA-BR-4279 
       26.70        11.70        19.56         7.43         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       34.68        32.78        25.61        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7851 
       31.20        32.94        24.76        23.93        28.01        12.43 
TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        9.07        17.49        12.26        20.55         8.05        12.95 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        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        19.17 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8592 
       15.85         3.72         1.12        12.79        13.45         6.28 
TCGA-BR-8680 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       15.81        12.56         6.08        13.41        13.51         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL TCGA-BR-A4QM 
       14.17        12.82         0.66        19.36        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A489 
        2.83         0.30         0.07         0.10         0.10        11.31 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 
       12.62         3.02         1.02        29.98        19.07        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        0.00         9.01         6.97         0.99         6.02       105.07 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 
       15.02        65.10        21.07        18.61        17.85        12.79 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A748 
       17.19        18.21        13.78        14.76        11.44         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        7.13         0.62        21.27        59.54         5.03        13.58 
TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
       18.08        11.41         5.59        11.84        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8462 
       29.98         6.51        19.36         8.88         8.81        18.81 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-AB1V 
        5.36        13.08         1.41         6.44         6.51         7.82 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
        3.72        19.73         4.60         9.24        11.05         5.13 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA 
      122.30        40.64       116.38        71.38        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
        0.92        48.79        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       28.96        34.29        16.31         1.87         9.27        23.41 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A924 
       13.35        26.24        11.70        61.22        20.81        55.43 
TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6I 
        6.58         2.66        22.09        28.41        17.13        16.14 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.00 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            115.69             122.30 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             12.71              13.08 
[1] "0.1 - 115.7 (12.7)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         2        9       23       17        23        37
  20Q GAIN WILD-TYPE       1        5       18       14        15        18
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           4         62         41         24       24
  20Q GAIN WILD-TYPE         0         23         21         17       22
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   2                  1
  STAGE IA                  9                  5
  STAGE IB                 23                 18
  STAGE II                 17                 14
  STAGE IIA                23                 15
  STAGE IIB                37                 18
  STAGE III                 4                  0
  STAGE IIIA               62                 23
  STAGE IIIB               41                 21
  STAGE IIIC               24                 17
  STAGE IV                 24                 22
[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    11  59 132  68
  20Q GAIN WILD-TYPE  11  31  63  51
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               11                 11
  T2               59                 31
  T3              132                 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   73 82 59 51
  20Q GAIN WILD-TYPE 56 36 25 38
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               73                 56
  N1               82                 36
  N2               59                 25
  N3               51                 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"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   246  15
  20Q GAIN WILD-TYPE 141  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    246   15
  20Q GAIN WILD-TYPE  141   15
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              246                141
  1               15                 15
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    86 190
  20Q GAIN WILD-TYPE  72  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     86  190
  20Q GAIN WILD-TYPE   72   88
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               86                 72
  MALE                190                 88
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  20Q GAIN MUTATED                                      32
  20Q GAIN WILD-TYPE                                    39
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                       96
  20Q GAIN WILD-TYPE                                                     66
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                                  60
  20Q GAIN WILD-TYPE                                                                21
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  20Q GAIN MUTATED                                                 61
  20Q GAIN WILD-TYPE                                               17
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  20Q GAIN MUTATED                                                         11
  20Q GAIN WILD-TYPE                                                       10
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  20Q GAIN MUTATED                                                           6
  20Q GAIN WILD-TYPE                                                         2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  20Q GAIN MUTATED                                          8
  20Q GAIN WILD-TYPE                                        5
D37V8, multiclass
                                                                   clus
vv                                                                  20Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         8
                                                                   clus
vv                                                                  20Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             39
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            66
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           5
[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"
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3 273
  20Q GAIN WILD-TYPE   3 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  273
  20Q GAIN WILD-TYPE    3  157
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 3                  3
  YES              273                157
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   226   9  10  14
  20Q GAIN WILD-TYPE 121   9   9  11
D37V10, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              226                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                         2
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           1   170
  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                  2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  170                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     3 198
  20Q GAIN WILD-TYPE   1 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  198
  20Q GAIN WILD-TYPE    1  115
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO              198                115
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    12   7
  21Q GAIN WILD-TYPE 242 143
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                385 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                143 
$`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        12.95         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         3.25         3.42        10.26        15.22 
TCGA-D7-6822 TCGA-D7-A6F0 TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4HD 
       12.33         2.96         5.92        22.75        11.77        27.42 
TCGA-IN-A6RP 
        6.44 

$`21Q GAIN WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.56         2.66        16.31        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50        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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
        9.86        15.68        10.68        12.56         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        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        12.82         0.66        19.36 
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        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       11.57         5.13         2.83        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         9.34        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         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       14.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
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-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        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 
       10.55        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        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44         9.76        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        7.40         7.13         0.62         7.99        16.24        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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
        5.52         0.23        18.08        26.47         1.51        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        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 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        12.30         9.67         8.88         8.81        21.21 
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         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         1.41         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       20.15        37.64         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        61.25         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-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        36.16         7.36         9.50         9.73        52.24 
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-A94U 
       64.18        21.04         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        40.08        28.41        32.94        29.98        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        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.69               0.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             27.42             122.30 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             10.26              12.95 
[1] "0.7 - 27.4 (10.3)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.5"
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       3       12       38       28        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           0          1          2          3        1
  21Q GAIN WILD-TYPE         4         84         60         38       45
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  2                 12
  STAGE IB                  3                 38
  STAGE II                  3                 28
  STAGE IIA                 2                 36
  STAGE IIB                 4                 51
  STAGE III                 0                  4
  STAGE IIIA                1                 84
  STAGE IIIB                2                 60
  STAGE IIIC                3                 38
  STAGE IV                  1                 45
[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   8   5
  21Q GAIN WILD-TYPE  19  85 187 114
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                 19
  T2                5                 85
  T3                8                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   6   3   3
  21Q GAIN WILD-TYPE 120 112  81  86
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                9                120
  N1                6                112
  N2                3                 81
  N3                3                 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"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    20   1
  21Q GAIN WILD-TYPE 367  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     20    1
  21Q GAIN WILD-TYPE  367   29
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               20                367
  1                1                 29
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     8  13
  21Q GAIN WILD-TYPE 150 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8   13
  21Q GAIN WILD-TYPE  150  265
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                8                150
  MALE                 13                265
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  21Q GAIN MUTATED                                       1
  21Q GAIN WILD-TYPE                                    70
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                       10
  21Q GAIN WILD-TYPE                                                    152
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                                   3
  21Q GAIN WILD-TYPE                                                                78
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  21Q GAIN MUTATED                                                  6
  21Q GAIN WILD-TYPE                                               72
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  21Q GAIN MUTATED                                                          0
  21Q GAIN WILD-TYPE                                                       21
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  21Q GAIN MUTATED                                                           1
  21Q GAIN WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  21Q GAIN MUTATED                                          0
  21Q GAIN WILD-TYPE                                       13
D38V8, multiclass
                                                                   clus
vv                                                                  21Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  21Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             70
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           152
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 78
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  72
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          13
[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"
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  21
  21Q GAIN WILD-TYPE   6 409
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   21
  21Q GAIN WILD-TYPE    6  409
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                  6
  YES               21                409
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    17   1   1   0
  21Q GAIN WILD-TYPE 330  17  18  25
D38V10, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               17                330
  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                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           0    14
  21Q GAIN WILD-TYPE                                         1   260
D38V12, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                                    6                 82
  BLACK OR AFRICAN AMERICAN                                0                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                260
[1] 4 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   4 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   20
  21Q GAIN WILD-TYPE    4  293
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               20                293
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    20  11
  22Q GAIN WILD-TYPE 234 139
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                373 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                11                139 
$`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        18.71        20.22 
TCGA-BR-A452 TCGA-BR-A4J8 TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8528 TCGA-CG-4436 
        7.53        13.51         3.25         0.07         0.10         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         2.96        72.23 
TCGA-FP-7998 TCGA-HU-8604 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-IN-7808 
       22.29        12.10        11.77         6.25        12.30         3.45 
TCGA-IN-A6RO TCGA-KB-A6F7 TCGA-RD-A8N6 TCGA-VQ-A8PJ TCGA-VQ-A91D TCGA-VQ-AA68 
        1.41        60.56         8.94         2.70        11.70        40.08 
TCGA-VQ-AA6K 
       12.43 

$`22Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        6.97         7.43        18.35        30.90         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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        12.76        17.49        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         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 
       19.50        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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        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        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36         0.46        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       11.57         5.13         2.83        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        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 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       18.97         7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        79.07        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        12.36        12.66        11.93 
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        10.55        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        15.16 
TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        16.24        14.47        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
        5.92        14.27        12.59        14.17        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       19.36        23.84         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21        18.81         3.39        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G 
        1.81         7.82        13.51         2.53         5.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         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-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44        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        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       22.19         2.50        12.79        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
       23.41        15.65        13.35        26.24        27.35        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       14.33        65.16        36.69        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        52.24         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        64.18        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        22.09        18.41        28.41        32.94        29.98 
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        21.11        10.62 
TCGA-ZQ-A9CR 
        0.79 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.00 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             72.23             122.30 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             12.10              12.95 
[1] "0.1 - 72.2 (12.1)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1"  
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       3       10       36       29        36        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           1          6          3          4        1
  22Q GAIN WILD-TYPE         3         79         59         37       45
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  4                 10
  STAGE IB                  5                 36
  STAGE II                  2                 29
  STAGE IIA                 2                 36
  STAGE IIB                 3                 52
  STAGE III                 1                  3
  STAGE IIIA                6                 79
  STAGE IIIB                3                 59
  STAGE IIIC                4                 37
  STAGE IV                  1                 45
[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  18  80 186 111
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                4                 18
  T2               10                 80
  T3                9                186
  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 117 112  78  82
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               12                117
  N1                6                112
  N2                6                 78
  N3                7                 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"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    29   2
  22Q GAIN WILD-TYPE 358  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     29    2
  22Q GAIN WILD-TYPE  358   28
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               29                358
  1                2                 28
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    13  19
  22Q GAIN WILD-TYPE 145 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     13   19
  22Q GAIN WILD-TYPE  145  259
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               13                145
  MALE                 19                259
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  22Q GAIN MUTATED                                       5
  22Q GAIN WILD-TYPE                                    66
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                        8
  22Q GAIN WILD-TYPE                                                    154
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                                   7
  22Q GAIN WILD-TYPE                                                                74
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  22Q GAIN MUTATED                                                  7
  22Q GAIN WILD-TYPE                                               71
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  22Q GAIN MUTATED                                                          3
  22Q GAIN WILD-TYPE                                                       18
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  22Q GAIN MUTATED                                                           1
  22Q GAIN WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  22Q GAIN MUTATED                                          1
  22Q GAIN WILD-TYPE                                       12
D39V8, multiclass
                                                                   clus
vv                                                                  22Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  22Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 74
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  71
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          12
[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"
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  32
  22Q GAIN WILD-TYPE   6 398
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   32
  22Q GAIN WILD-TYPE    6  398
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                  6
  YES               32                398
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    27   1   1   1
  22Q GAIN WILD-TYPE 320  17  18  24
D39V10, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               27                320
  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                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    19
  22Q GAIN WILD-TYPE                                         1   255
D39V12, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                                    9                 79
  BLACK OR AFRICAN AMERICAN                                1                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   19                255
[1] 4 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   3 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   25
  22Q GAIN WILD-TYPE    3  288
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               25                288
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    23  21
  XP GAIN WILD-TYPE 231 129
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               44               360 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               21               129 
$`XP GAIN MUTATED`
TCGA-BR-4187 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7717 TCGA-BR-8058 TCGA-BR-8059 
        4.64        21.11         9.21        18.15        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8365 TCGA-BR-8678 TCGA-BR-A452 TCGA-BR-A4CS TCGA-CD-8528 
        0.69        17.52        11.54         7.53         1.48         0.10 
TCGA-CD-A487 TCGA-CD-A4MG TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4460 TCGA-CG-4472 
        9.34         6.58         3.02         7.99        21.99        12.00 
TCGA-CG-5718 TCGA-CG-5726 TCGA-CG-5727 TCGA-D7-6519 TCGA-D7-8576 TCGA-D7-A6EV 
       36.00        28.96        79.07        20.55        14.66        11.24 
TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-HU-8244 
        2.96         0.62         7.99        72.23         3.48        14.27 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4HD 
       24.30        12.30        24.20        25.81         6.51        27.42 
TCGA-R5-A7ZE TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8PY TCGA-VQ-A91E 
       18.21         8.94        48.79        18.48        14.33        11.93 
TCGA-VQ-A91Q TCGA-VQ-A91U 
       20.81         1.71 

$`XP GAIN WILD-TYPE`
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-4267 
        6.61         6.97         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        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-6802 
       25.61        18.05        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        32.94        12.82        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       15.42        28.01        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
        9.07        12.76        18.71        11.44        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
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        19.50        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        19.17        14.79         0.26        15.85 
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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       10.68        12.56        13.87         6.08        22.26        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        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 
       12.82         0.66        19.36        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        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         3.42        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        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 
       12.36        12.66        11.93        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        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       13.71        11.31        11.44         9.76        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 
        4.34         7.40         7.13        16.24        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC 
       12.10        10.62         0.76         5.59        11.84         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 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        12.30         9.67         8.88         8.81        21.21 
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         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.08         1.41         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        5.56         1.81         7.82        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
       60.56        20.15        37.64         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67         8.52        61.25         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-A8DU TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        28.96        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-A8PU TCGA-VQ-A8PX 
       23.41        15.65        13.35        26.24        27.35        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       65.16        36.69        11.70        61.22        18.74        22.68 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       36.16         7.36         9.50         9.73        52.24         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        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
       21.04         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       40.08        28.41        32.94        29.98        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        21.11        12.43        10.62         0.79 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
              0.1               0.0 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            79.07            122.30 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           13.285            12.820 
[1] "0.1 - 79.1 (13.3)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         1        5        5        3         5         4
  XP GAIN WILD-TYPE       2        9       36       28        33        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED           1          7          7          1        7
  XP GAIN WILD-TYPE         3         78         55         40       39
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 5                 9
  STAGE IB                 5                36
  STAGE II                 3                28
  STAGE IIA                5                33
  STAGE IIB                4                51
  STAGE III                1                 3
  STAGE IIIA               7                78
  STAGE IIIB               7                55
  STAGE IIIC               1                40
  STAGE IV                 7                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
  XP GAIN MUTATED     5  11  18  13
  XP GAIN WILD-TYPE  17  79 177 106
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               5                17
  T2              11                79
  T3              18               177
  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  13   8   5
  XP GAIN WILD-TYPE 109 105  76  84
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              20               109
  N1              13               105
  N2               8                76
  N3               5                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"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    43   3
  XP GAIN WILD-TYPE 344  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     43    3
  XP GAIN WILD-TYPE  344   27
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              43               344
  1               3                27
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    23  25
  XP GAIN WILD-TYPE 135 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     23   25
  XP GAIN WILD-TYPE  135  253
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              23               135
  MALE                25               253
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  XP GAIN MUTATED                                       4
  XP GAIN WILD-TYPE                                    67
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XP GAIN MUTATED                                                       17
  XP GAIN WILD-TYPE                                                    145
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XP GAIN MUTATED                                                                  14
  XP GAIN WILD-TYPE                                                                67
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  XP GAIN MUTATED                                                 11
  XP GAIN WILD-TYPE                                               67
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  XP GAIN MUTATED                                                          0
  XP GAIN WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  XP GAIN MUTATED                                                           1
  XP GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  XP GAIN MUTATED                                          0
  XP GAIN WILD-TYPE                                       13
D40V8, multiclass
                                                                   clus
vv                                                                  XP GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  XP GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          145
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 67
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         13
[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"
D40V9, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0  48
  XP GAIN WILD-TYPE   6 382
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   48
  XP GAIN WILD-TYPE    6  382
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                0                 6
  YES              48               382
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    39   0   3   3
  XP GAIN WILD-TYPE 308  18  16  22
D40V10, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              39               308
  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"
D40V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XP GAIN MUTATED      12                         3
  XP GAIN WILD-TYPE    76                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP GAIN MUTATED                                           0    23
  XP GAIN WILD-TYPE                                         1   251
D40V12, multiclass
                                           clus
vv                                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                                  12                76
  BLACK OR AFRICAN AMERICAN                               3                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  23               251
[1] 4 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  34
  XP GAIN WILD-TYPE   4 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   34
  XP GAIN WILD-TYPE    4  279
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              34               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 225 128
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               51               353 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               22               128 
$`XQ GAIN MUTATED`
TCGA-BR-4187 TCGA-BR-6458 TCGA-BR-6801 TCGA-BR-7717 TCGA-BR-8058 TCGA-BR-8059 
        4.64        19.33        21.11        18.15        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8683 TCGA-BR-A452 TCGA-CD-8528 
        0.69        13.08        17.52         9.86         7.53         0.10 
TCGA-CD-A487 TCGA-CD-A4MG TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4460 TCGA-CG-4472 
        9.34         6.58         3.02         7.99        21.99        12.00 
TCGA-CG-5718 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5734 TCGA-D7-6526 TCGA-D7-6528 
       36.00        28.96        79.07         7.99        17.19        15.22 
TCGA-D7-6815 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 
       15.98        11.24         2.96        15.65         0.62         7.99 
TCGA-F1-6875 TCGA-FP-7735 TCGA-HU-8244 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G9 
       72.23         3.48        14.27        24.30        12.30        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4HD TCGA-IN-7808 TCGA-R5-A7O7 
       22.75        25.81         6.51        27.42         3.45        45.67 
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        11.93         1.71 
TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-AA68 
       52.24        64.18        40.08 

$`XQ GAIN WILD-TYPE`
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-4267 
        6.61         6.97         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
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-6802 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       15.42        28.01        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
        9.07        12.76        18.71        11.44        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         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        19.17        14.79         0.26        15.85         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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81        16.44        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        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 
       12.82         0.66        19.36        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        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         3.42        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        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-D7-5577 
       15.02        65.10         4.01        69.04        21.07        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85        13.35        10.26        12.79        10.55 
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-A6EX 
        5.92        15.16        13.78        14.76        13.71        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         8.38         4.34         7.40         7.13 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 
       16.24        14.47        21.27        11.38        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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        5.52         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        5.59        11.84         3.25        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.81        21.21        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         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         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        9.86        18.21         8.52        61.25         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-A8DU 
       35.61        16.87        19.04         5.79         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       27.88        32.48         7.73        28.96        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       22.19         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-A8PU 
        9.27        23.41        15.65        13.35        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N 
       64.57        65.16        36.69        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        22.68        36.16         7.36         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-A94U TCGA-VQ-AA64 
       21.04         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        32.94        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              0.1               0.0 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            79.07            122.30 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            14.43             12.79 
[1] "0.1 - 79.1 (14.4)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         1        5        7        2         5         7
  XQ GAIN WILD-TYPE       2        9       34       29        33        48
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           2          9          6          2        7
  XQ GAIN WILD-TYPE         2         76         56         39       39
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 5                 9
  STAGE IB                 7                34
  STAGE II                 2                29
  STAGE IIA                5                33
  STAGE IIB                7                48
  STAGE III                2                 2
  STAGE IIIA               9                76
  STAGE IIIB               6                56
  STAGE IIIC               2                39
  STAGE IV                 7                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
  XQ GAIN MUTATED     5  13  21  15
  XQ GAIN WILD-TYPE  17  77 174 104
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               5                17
  T2              13                77
  T3              21               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    21  18   9   5
  XQ GAIN WILD-TYPE 108 100  75  84
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              21               108
  N1              18               100
  N2               9                75
  N3               5                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"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    48   5
  XQ GAIN WILD-TYPE 339  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     48    5
  XQ GAIN WILD-TYPE  339   25
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              48               339
  1               5                25
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    26  29
  XQ GAIN WILD-TYPE 132 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     26   29
  XQ GAIN WILD-TYPE  132  249
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              26               132
  MALE                29               249
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  XQ GAIN MUTATED                                       4
  XQ GAIN WILD-TYPE                                    67
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                       16
  XQ GAIN WILD-TYPE                                                    146
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                                  14
  XQ GAIN WILD-TYPE                                                                67
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  XQ GAIN MUTATED                                                 18
  XQ GAIN WILD-TYPE                                               60
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  XQ GAIN MUTATED                                                          0
  XQ GAIN WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  XQ GAIN MUTATED                                                           1
  XQ GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  XQ GAIN MUTATED                                          1
  XQ GAIN WILD-TYPE                                       12
D41V8, multiclass
                                                                   clus
vv                                                                  XQ GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  XQ GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 60
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         12
[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"
D41V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  55
  XQ GAIN WILD-TYPE   6 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   55
  XQ GAIN WILD-TYPE    6  375
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                0                 6
  YES              55               375
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    45   0   3   3
  XQ GAIN WILD-TYPE 302  18  16  22
D41V10, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              45               302
  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      14                         2
  XQ GAIN WILD-TYPE    74                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           0    29
  XQ GAIN WILD-TYPE                                         1   245
D41V12, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                                  14                74
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  29               245
[1] 4 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  37
  XQ GAIN WILD-TYPE   3 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   37
  XQ GAIN WILD-TYPE    3  276
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              37               276
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    34  24
  1P LOSS WILD-TYPE 220 126
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               58               346 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               24               126 
$`1P LOSS MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7704 
       11.01         9.44         6.61        17.29        19.33        35.24 
TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-A452 
       18.71         2.66         9.21        11.54         9.86         7.53 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 
       20.65        20.42         1.15        13.64         3.25         0.30 
TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 
        0.07         0.13         3.42        11.31        20.02         3.02 
TCGA-CG-4438 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 
       54.08         1.02        12.03         4.01        11.93        20.55 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8573 TCGA-D7-A74A TCGA-EQ-5647 
       17.19        10.26        15.22        19.50         7.40         0.62 
TCGA-EQ-A4SO TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4HD TCGA-KB-A93H TCGA-MX-A663 
       16.24        14.17        12.10        27.42        37.64         9.86 
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        36.69        52.24         4.54        64.18        21.04 
TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       11.24        29.98        12.43         0.79 

$`1P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05         0.56        12.95        16.31         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        19.50        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        19.17        14.79         0.26        15.85 
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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         6.08        22.26         1.48        13.41        13.51 
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        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        19.36        13.51         0.46        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        2.83        13.15        13.18         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         9.34        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.20         0.10        12.62        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        7.99         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        69.04        21.07         7.99        12.36 
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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       13.35        15.98        12.79        10.55        11.31        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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
        2.96        15.65         8.38         4.34         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-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        14.27        12.59        11.41        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        8.81        21.21         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
        5.36         5.19        13.08         1.41         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         5.56         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        20.15         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67         8.52        61.25         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        16.31         2.50        12.79 
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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       26.24        27.35        64.57        14.33        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.93        61.22        18.74        20.81        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 
       36.16         7.36         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-A94U 
       55.43         6.58         5.72         2.66        42.54        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        40.08        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        16.14        21.11        10.62 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.00 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            64.18            122.30 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            11.98             12.95 
[1] "0.1 - 64.2 (12.0)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.3"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         0        0        5        6         7         6
  1P LOSS WILD-TYPE       3       14       36       25        31        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           0         12          8          4       10
  1P LOSS WILD-TYPE         4         73         54         37       36
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 0                14
  STAGE IB                 5                36
  STAGE II                 6                25
  STAGE IIA                7                31
  STAGE IIB                6                49
  STAGE III                0                 4
  STAGE IIIA              12                73
  STAGE IIIB               8                54
  STAGE IIIC               4                37
  STAGE IV                10                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
  1P LOSS MUTATED     0  11  29  19
  1P LOSS WILD-TYPE  22  79 166 100
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               0                22
  T2              11                79
  T3              29               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
  1P LOSS MUTATED    17  14  14  11
  1P LOSS WILD-TYPE 112 104  70  78
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              17               112
  N1              14               104
  N2              14                70
  N3              11                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"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    49   8
  1P LOSS WILD-TYPE 338  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     49    8
  1P LOSS WILD-TYPE  338   22
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              49               338
  1               8                22
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    22  37
  1P LOSS WILD-TYPE 136 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     22   37
  1P LOSS WILD-TYPE  136  241
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              22               136
  MALE                37               241
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1P LOSS MUTATED                                       4
  1P LOSS WILD-TYPE                                    67
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                       18
  1P LOSS WILD-TYPE                                                    144
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                                  13
  1P LOSS WILD-TYPE                                                                68
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  1P LOSS MUTATED                                                 18
  1P LOSS WILD-TYPE                                               60
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  1P LOSS MUTATED                                                          3
  1P LOSS WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  1P LOSS MUTATED                                                           1
  1P LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  1P LOSS MUTATED                                          2
  1P LOSS WILD-TYPE                                       11
D42V8, multiclass
                                                                   clus
vv                                                                  1P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  1P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          144
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 60
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         11
[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"
D42V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  59
  1P LOSS WILD-TYPE   6 371
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   59
  1P LOSS WILD-TYPE    6  371
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                0                 6
  YES              59               371
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    40   2   8   2
  1P LOSS WILD-TYPE 307  16  11  23
D42V10, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              40               307
  R1               2                16
  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      12                         2
  1P LOSS WILD-TYPE    76                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           1    36
  1P LOSS WILD-TYPE                                         0   238
D42V12, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                                  12                76
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  36               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"
D42V13, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  39
  1P LOSS WILD-TYPE   4 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   39
  1P LOSS WILD-TYPE    4  274
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              39               274
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    15  13
  1Q LOSS WILD-TYPE 239 137
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               376 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13               137 
$`1Q LOSS MUTATED`
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-8289 
        9.44         6.61        17.29        19.33        35.24         2.66 
TCGA-BR-A4PD TCGA-CD-5799 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CG-5724 
       20.65         3.25         3.42        11.31        12.43        12.03 
TCGA-CG-5730 TCGA-D7-6519 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-HU-8604 TCGA-HU-A4HD 
        4.01        20.55         7.40        16.24        12.10        27.42 
TCGA-IN-8663 TCGA-IP-7968 TCGA-KB-A93H TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PE 
        3.39         2.53        37.64        13.25        13.02        22.19 
TCGA-VQ-A925 TCGA-VQ-AA6B TCGA-VQ-AA6K TCGA-ZQ-A9CR 
        4.54        29.98        12.43         0.79 

$`1Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4184 
       26.70        11.70        19.56        11.01         9.47         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
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        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51         0.46        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
       13.64        11.57         5.13         2.83        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.10         9.34        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5732 
      105.07        15.02        28.96        79.07        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        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        10.55        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 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         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-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       59.54         5.03        13.58         0.56         5.52         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        11.41        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        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 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        1.41         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        1.81         7.82        13.51         5.56        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73         9.86        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         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-A8E0 
       19.04         5.79         0.92        48.79         5.46        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        16.31         2.50        12.79 
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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       13.35        26.24        27.35        64.57        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       36.69        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       22.68         1.71        36.16         7.36         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       52.24         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
       64.18        21.04         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        40.08        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        16.14        21.11        10.62 

  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 
           12.265            12.920 
[1] "0.8 - 37.6 (12.3)"  "0.0 - 122.3 (12.9)"
[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         6
  1Q LOSS WILD-TYPE       3       14       40       29        34        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           0          5          4          2        4
  1Q LOSS WILD-TYPE         4         80         58         39       42
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 0                14
  STAGE IB                 1                40
  STAGE II                 2                29
  STAGE IIA                4                34
  STAGE IIB                6                49
  STAGE III                0                 4
  STAGE IIIA               5                80
  STAGE IIIB               4                58
  STAGE IIIC               2                39
  STAGE IV                 4                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
  1Q LOSS MUTATED     0   5  16   7
  1Q LOSS WILD-TYPE  22  85 179 112
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               0                22
  T2               5                85
  T3              16               179
  T4               7               112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q LOSS MUTATED     7   8   6   6
  1Q LOSS WILD-TYPE 122 110  78  83
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               7               122
  N1               8               110
  N2               6                78
  N3               6                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    21   4
  1Q LOSS WILD-TYPE 366  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     21    4
  1Q LOSS WILD-TYPE  366   26
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              21               366
  1               4                26
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    11  17
  1Q LOSS WILD-TYPE 147 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11   17
  1Q LOSS WILD-TYPE  147  261
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11               147
  MALE                17               261
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1Q LOSS MUTATED                                       3
  1Q LOSS WILD-TYPE                                    68
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                       10
  1Q LOSS WILD-TYPE                                                    152
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                                   6
  1Q LOSS WILD-TYPE                                                                75
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  1Q LOSS MUTATED                                                  7
  1Q LOSS WILD-TYPE                                               71
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  1Q LOSS MUTATED                                                          0
  1Q LOSS WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  1Q LOSS MUTATED                                                           0
  1Q LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  1Q LOSS MUTATED                                          2
  1Q LOSS WILD-TYPE                                       11
D43V8, multiclass
                                                                   clus
vv                                                                  1Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  1Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                75
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 71
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         11
[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"
D43V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  28
  1Q LOSS WILD-TYPE   6 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   28
  1Q LOSS WILD-TYPE    6  402
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                0                 6
  YES              28               402
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    17   1   4   1
  1Q LOSS WILD-TYPE 330  17  15  24
D43V10, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              17               330
  R1               1                17
  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                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0    18
  1Q LOSS WILD-TYPE                                         1   256
D43V12, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                                   7                81
  BLACK OR AFRICAN AMERICAN                               1                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  18               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"
D43V13, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  19
  1Q LOSS WILD-TYPE   4 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   19
  1Q LOSS WILD-TYPE    4  294
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              19               294
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    11  11
  2P LOSS WILD-TYPE 243 139
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               22               382 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               139 
$`2P LOSS MUTATED`
TCGA-BR-6565 TCGA-BR-8060 TCGA-BR-8687 TCGA-CD-8535 TCGA-CD-A48A TCGA-CG-4475 
        9.17        11.44         8.22         0.13        12.43        22.98 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 TCGA-HJ-7597 
       12.66        11.93        17.19        15.22        14.66        26.47 
TCGA-HU-8243 TCGA-HU-A4GU TCGA-IN-A6RL TCGA-RD-A7C1 TCGA-RD-A8N9 TCGA-VQ-A8DU 
        5.92         6.25         5.19        16.67        35.61         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8PJ TCGA-VQ-A8PU TCGA-VQ-A91Z 
       18.48         2.70        27.35        52.24 

$`2P LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        12.95         2.66        16.31         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        19.50        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        19.17        14.79         0.26        15.85 
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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        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        12.82         0.66        19.36        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        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42         9.34        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 
        0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         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-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 
       69.04        21.07         7.99        12.36        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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.99        16.24        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-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
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-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        8.88         8.81        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
        3.39        18.38         5.36        13.08         1.41         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         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
       13.51         2.53         5.56        60.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73         9.86        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         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        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        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        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        7.36         9.50         9.73         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        64.18        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.54        11.24        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       32.94        29.98        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.13              0.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            52.24            122.30 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           12.545            12.855 
[1] "0.1 - 52.2 (12.5)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.4"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        0        4        2         1         4
  2P LOSS WILD-TYPE       3       14       37       29        37        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           0          9          1          3        2
  2P LOSS WILD-TYPE         4         76         61         38       44
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 0                14
  STAGE IB                 4                37
  STAGE II                 2                29
  STAGE IIA                1                37
  STAGE IIB                4                51
  STAGE III                0                 4
  STAGE IIIA               9                76
  STAGE IIIB               1                61
  STAGE IIIC               3                38
  STAGE IV                 2                44
[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   8  12   6
  2P LOSS WILD-TYPE  22  82 183 113
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                22
  T2               8                82
  T3              12               183
  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
  2P LOSS MUTATED     7   7   8   4
  2P LOSS WILD-TYPE 122 111  76  85
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               7               122
  N1               7               111
  N2               8                76
  N3               4                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"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    23   1
  2P LOSS WILD-TYPE 364  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     23    1
  2P LOSS WILD-TYPE  364   29
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              23               364
  1               1                29
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    12  14
  2P LOSS WILD-TYPE 146 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     12   14
  2P LOSS WILD-TYPE  146  264
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              12               146
  MALE                14               264
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  2P LOSS MUTATED                                       4
  2P LOSS WILD-TYPE                                    67
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                        8
  2P LOSS WILD-TYPE                                                    154
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                                   1
  2P LOSS WILD-TYPE                                                                80
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  2P LOSS MUTATED                                                  9
  2P LOSS WILD-TYPE                                               69
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  2P LOSS MUTATED                                                          2
  2P LOSS WILD-TYPE                                                       19
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  2P LOSS MUTATED                                                           0
  2P LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  2P LOSS MUTATED                                          1
  2P LOSS WILD-TYPE                                       12
D44V8, multiclass
                                                                   clus
vv                                                                  2P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  2P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                80
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 69
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         12
[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"
D44V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2  24
  2P LOSS WILD-TYPE   4 406
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   24
  2P LOSS WILD-TYPE    4  406
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                2                 4
  YES              24               406
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    21   3   1   0
  2P LOSS WILD-TYPE 326  15  18  25
D44V10, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              21               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"
D44V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED       6                         1
  2P LOSS WILD-TYPE    82                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           0    15
  2P LOSS WILD-TYPE                                         1   259
D44V12, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                                   6                82
  BLACK OR AFRICAN AMERICAN                               1                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  15               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"
D44V13, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  18
  2P LOSS WILD-TYPE   4 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   18
  2P LOSS WILD-TYPE    4  295
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              18               295
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    16  13
  2Q LOSS WILD-TYPE 238 137
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               29               375 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               137 
$`2Q LOSS MUTATED`
TCGA-BR-6565 TCGA-BR-8687 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4300 
        9.17         8.22         0.13         3.42        12.43        20.02 
TCGA-CG-4475 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 
       22.98        12.66        11.93        17.19        15.22        14.66 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-A6RL 
       26.47         5.92        22.75         6.25        27.42         5.19 
TCGA-IN-A6RO TCGA-IN-AB1V TCGA-R5-A7ZE TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ 
        1.41         7.82        18.21        35.61         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8PJ TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-VQ-AA68 
       18.48         2.70        27.35        22.09        40.08 

$`2Q LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
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        19.50        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        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        12.82         0.66        19.36 
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        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.10         9.34        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 
        0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        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        12.36        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
       18.54        18.61        17.85        13.35        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        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        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34         7.40         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        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-A8CX TCGA-HF-A5NB TCGA-HU-8238 
       13.58         0.56         5.52         0.23        18.08         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        1.81        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       37.64         3.72        19.73         9.86        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         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        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        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        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        7.36         9.50         9.73        52.24         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        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        42.54        11.24        18.41        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       29.98        17.13        54.12        26.04        16.14        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        10.62         0.79 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.13              0.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            40.08            122.30 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            13.02             12.82 
[1] "0.1 - 40.1 (13.0)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         0        2        3        2         2         5
  2Q LOSS WILD-TYPE       3       12       38       29        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           0         10          2          4        3
  2Q LOSS WILD-TYPE         4         75         60         37       43
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 2                12
  STAGE IB                 3                38
  STAGE II                 2                29
  STAGE IIA                2                36
  STAGE IIB                5                50
  STAGE III                0                 4
  STAGE IIIA              10                75
  STAGE IIIB               2                60
  STAGE IIIC               4                37
  STAGE IV                 3                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
  2Q LOSS MUTATED     2   6  16   9
  2Q LOSS WILD-TYPE  20  84 179 110
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               2                20
  T2               6                84
  T3              16               179
  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
  2Q LOSS MUTATED    10   7  10   6
  2Q LOSS WILD-TYPE 119 111  74  83
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              10               119
  N1               7               111
  N2              10                74
  N3               6                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"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    29   2
  2Q LOSS WILD-TYPE 358  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     29    2
  2Q LOSS WILD-TYPE  358   28
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              29               358
  1               2                28
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    11  22
  2Q LOSS WILD-TYPE 147 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11   22
  2Q LOSS WILD-TYPE  147  256
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              11               147
  MALE                22               256
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  2Q LOSS MUTATED                                       4
  2Q LOSS WILD-TYPE                                    67
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                       10
  2Q LOSS WILD-TYPE                                                    152
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                                   1
  2Q LOSS WILD-TYPE                                                                80
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  2Q LOSS MUTATED                                                 12
  2Q LOSS WILD-TYPE                                               66
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  2Q LOSS MUTATED                                                          2
  2Q LOSS WILD-TYPE                                                       19
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  2Q LOSS MUTATED                                                           0
  2Q LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  2Q LOSS MUTATED                                          3
  2Q LOSS WILD-TYPE                                       10
D45V8, multiclass
                                                                   clus
vv                                                                  2Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  2Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                80
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 66
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         10
[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"
D45V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  31
  2Q LOSS WILD-TYPE   4 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   31
  2Q LOSS WILD-TYPE    4  399
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2                 4
  YES              31               399
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    25   3   2   0
  2Q LOSS WILD-TYPE 322  15  17  25
D45V10, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              25               322
  R1               3                15
  R2               2                17
  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      10                         2
  2Q LOSS WILD-TYPE    78                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           0    15
  2Q LOSS WILD-TYPE                                         1   259
D45V12, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                                  10                78
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  15               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"
D45V13, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  21
  2Q LOSS WILD-TYPE   4 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   21
  2Q LOSS WILD-TYPE    4  292
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              21               292
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    53  34
  3P LOSS WILD-TYPE 201 116
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               87               317 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               34               116 
$`3P LOSS MUTATED`
TCGA-B7-A5TJ TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 
       11.01        17.29        19.33        31.20        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8289 
       28.01         9.07        18.71        17.49         0.69         2.66 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8686 TCGA-BR-8687 
        5.39        25.18         9.21        20.22        15.68         8.22 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 
        7.53        22.26         1.48        12.89         0.72         0.53 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8527 TCGA-CD-8533 
       13.51        20.42         1.15        13.64         0.07         0.13 
TCGA-CD-A48A TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       12.43        20.02         7.99         8.05        54.08         4.01 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-6521 
       12.03        18.97        15.02         4.01        12.66        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-A6EX TCGA-EQ-5647 TCGA-EQ-8122 
       13.35        17.19        15.22        11.31         0.62         7.99 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8245 
       19.53        14.07        17.06         0.56         5.52        12.59 
TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-IN-7806 TCGA-IN-A6RO 
       14.17         3.25         6.25        23.84        21.21         1.41 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 
        6.44        12.59         6.51         5.56        37.64         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7C1 TCGA-RD-A8N6 TCGA-SW-A7EB 
       45.67        18.21         8.52        16.67         8.94         5.79 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PY 
       13.25        18.48        34.45        22.19         2.70        14.33 
TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6A 
        9.50         4.54        42.54        22.09        18.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       29.98        12.43         0.79 

$`3P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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        21.11        30.90        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       12.82         9.21        24.76        23.93        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 
       28.73        12.43         3.45        12.76        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.26        15.85         3.72         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44         9.86        10.68        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        6.08        13.41        13.51         8.98        14.17        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        19.36         0.46        20.65        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
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         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 
        3.02        27.02        15.95         1.02        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       47.05        19.07        21.99         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        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-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        69.04        21.07         7.99        12.36 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        10.55        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-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        2.96        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB 
       22.29        59.54         5.03        13.58         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51         5.92        14.27        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20        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        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        5.19        13.08         6.74         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        60.56        20.15         3.72        19.73 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         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-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44        35.61        16.87        19.04         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       48.79         5.46        13.02        35.24        21.73        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       15.65        13.35        26.24        27.35        64.57        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       36.69        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       22.68         1.71        36.16         7.36         9.73        52.24 
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        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D 
       21.04         2.66        11.24        40.08        28.41        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       54.12        26.04        16.14        21.11        10.62 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.00 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            54.08            122.30 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            12.89             12.82 
[1] "0.1 - 54.1 (12.9)"  "0.0 - 122.3 (12.8)"
[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        5         7        12
  3P LOSS WILD-TYPE       3       11       33       26        31        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           0         21         12          8       12
  3P LOSS WILD-TYPE         4         64         50         33       34
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 3                11
  STAGE IB                 8                33
  STAGE II                 5                26
  STAGE IIA                7                31
  STAGE IIB               12                43
  STAGE III                0                 4
  STAGE IIIA              21                64
  STAGE IIIB              12                50
  STAGE IIIC               8                33
  STAGE IV                12                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
  3P LOSS MUTATED     4  16  41  27
  3P LOSS WILD-TYPE  18  74 154  92
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               4                18
  T2              16                74
  T3              41               154
  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  22  29  14
  3P LOSS WILD-TYPE 107  96  55  75
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              22               107
  N1              22                96
  N2              29                55
  N3              14                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"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    73  10
  3P LOSS WILD-TYPE 314  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     73   10
  3P LOSS WILD-TYPE  314   20
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              73               314
  1              10                20
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    32  57
  3P LOSS WILD-TYPE 126 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     32   57
  3P LOSS WILD-TYPE  126  221
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              32               126
  MALE                57               221
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3P LOSS MUTATED                                       8
  3P LOSS WILD-TYPE                                    63
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                       32
  3P LOSS WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                                  24
  3P LOSS WILD-TYPE                                                                57
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  3P LOSS MUTATED                                                 17
  3P LOSS WILD-TYPE                                               61
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3P LOSS MUTATED                                                          4
  3P LOSS WILD-TYPE                                                       17
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  3P LOSS MUTATED                                                           1
  3P LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3P LOSS MUTATED                                          3
  3P LOSS WILD-TYPE                                       10
D46V8, multiclass
                                                                   clus
vv                                                                  3P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  3P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                57
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         10
[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"
D46V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  88
  3P LOSS WILD-TYPE   5 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   88
  3P LOSS WILD-TYPE    5  342
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                1                 5
  YES              88               342
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    73   3   5   1
  3P LOSS WILD-TYPE 274  15  14  24
D46V10, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              73               274
  R1               3                15
  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"
D46V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED      16                         2
  3P LOSS WILD-TYPE    72                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           0    59
  3P LOSS WILD-TYPE                                         1   215
D46V12, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                                  16                72
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  59               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"
D46V13, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  62
  3P LOSS WILD-TYPE   3 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   62
  3P LOSS WILD-TYPE    3  251
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              62               251
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    33  19
  3Q LOSS WILD-TYPE 221 131
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               52               352 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19               131 
$`3Q LOSS MUTATED`
TCGA-B7-A5TJ TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7959 
       11.01        17.29        35.24        15.42        28.01        18.71 
TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8687 
        0.69         2.66         5.39         9.21        20.22         8.22 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF 
        7.53        22.26        12.89         0.72        13.51         1.15 
TCGA-BR-A4QI TCGA-CD-A48A TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-5725 
       13.64        12.43        54.08         4.01        18.97        15.02 
TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-A6EX TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-8099 
       12.66        17.19        11.31         0.62        19.53        17.06 
TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GU TCGA-IN-7806 TCGA-IN-A6RO TCGA-IN-A6RS 
        5.52        14.17         6.25        21.21         1.41        12.59 
TCGA-IN-A7NR TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        6.51         5.56        37.64         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PY TCGA-VQ-A91X 
        8.52        13.25        34.45        22.19        14.33         9.50 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA6B TCGA-VQ-AA6K 
       42.54        22.09        29.98        12.43 

$`3Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       12.76        17.49        14.43        11.44        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05         0.56        12.95        16.31         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        19.50        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        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        25.18         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68        10.68        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08         1.48        13.41        13.51         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82         0.66        19.36         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.42        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.13         0.13         0.10         3.42         9.34        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         0.10        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-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       14.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01         7.07        12.00        22.98        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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        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        12.36        11.93        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-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        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-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
        9.76         2.96        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         7.99        16.24        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       11.38         3.48        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58         0.56         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        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        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        8.81        27.42         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-A7NT 
        5.36         5.19        13.08         6.44         6.74         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G 
        1.81         7.82        13.51         2.53        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        3.72        19.73        61.25         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-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        5.46        13.02        18.48        35.24        21.73        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        34.29        46.26        16.31 
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-A8PU TCGA-VQ-A8PX 
       23.41        15.65        13.35        26.24        27.35        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y 
       20.81        22.68         1.71        36.16         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       52.24         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        64.18        21.04         2.66        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       40.08        28.41        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        10.62         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 
            13.38             12.79 
[1] "0.6 - 54.1 (13.4)"  "0.0 - 122.3 (12.8)"
[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       3       11       38       30        33        46
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           0         13          6          4        9
  3Q LOSS WILD-TYPE         4         72         56         37       37
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 3                11
  STAGE IB                 3                38
  STAGE II                 1                30
  STAGE IIA                5                33
  STAGE IIB                9                46
  STAGE III                0                 4
  STAGE IIIA              13                72
  STAGE IIIB               6                56
  STAGE IIIC               4                37
  STAGE IV                 9                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
  3Q LOSS MUTATED     3   3  29  18
  3Q LOSS WILD-TYPE  19  87 166 101
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               3                19
  T2               3                87
  T3              29               166
  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
  3Q LOSS MUTATED    14  14  15   9
  3Q LOSS WILD-TYPE 115 104  69  80
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              14               115
  N1              14               104
  N2              15                69
  N3               9                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"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    46   7
  3Q LOSS WILD-TYPE 341  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     46    7
  3Q LOSS WILD-TYPE  341   23
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              46               341
  1               7                23
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    20  34
  3Q LOSS WILD-TYPE 138 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     20   34
  3Q LOSS WILD-TYPE  138  244
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              20               138
  MALE                34               244
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3Q LOSS MUTATED                                       2
  3Q LOSS WILD-TYPE                                    69
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                       23
  3Q LOSS WILD-TYPE                                                    139
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                                  13
  3Q LOSS WILD-TYPE                                                                68
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  3Q LOSS MUTATED                                                 11
  3Q LOSS WILD-TYPE                                               67
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3Q LOSS MUTATED                                                          2
  3Q LOSS WILD-TYPE                                                       19
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  3Q LOSS MUTATED                                                           0
  3Q LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3Q LOSS MUTATED                                          3
  3Q LOSS WILD-TYPE                                       10
D47V8, multiclass
                                                                   clus
vv                                                                  3Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  3Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            69
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 67
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         10
[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"
D47V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  54
  3Q LOSS WILD-TYPE   6 376
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   54
  3Q LOSS WILD-TYPE    6  376
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                 6
  YES              54               376
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    43   3   2   1
  3Q LOSS WILD-TYPE 304  15  17  24
D47V10, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              43               304
  R1               3                15
  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"
D47V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED       8                         1
  3Q LOSS WILD-TYPE    80                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           0    40
  3Q LOSS WILD-TYPE                                         1   234
D47V12, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                                   8                80
  BLACK OR AFRICAN AMERICAN                               1                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  40               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"
D47V13, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  38
  3Q LOSS WILD-TYPE   3 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   38
  3Q LOSS WILD-TYPE    3  275
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              38               275
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    92  60
  4P LOSS WILD-TYPE 162  90
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              152               252 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               60                90 
$`4P LOSS MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6565 
       11.01         9.44         6.61         9.57        17.29         9.17 
TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 
       31.20         9.21        35.24        18.15        28.73         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 
       18.71        17.49         0.69         9.60         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20        15.58         7.40        19.50        22.19        17.52 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
       14.04        14.79         3.72         5.39         9.21        20.22 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ 
        0.49        11.54         9.86        10.68         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI 
        1.48         0.72         0.66        13.51        20.65        13.64 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8532 
        3.25         0.30         0.07         0.07         0.07         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.13         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       12.20        20.02         7.99         8.05        54.08         4.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       47.05        19.07        12.03        18.97         7.07        30.97 
TCGA-CG-5725 TCGA-CG-5727 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 
       15.02        79.07        19.13        20.55        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX 
       15.22        11.31        19.50        18.21        16.44        11.31 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 
        7.40         0.62         7.99        11.38        14.07        17.06 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 
        5.52         0.23        26.47         1.51         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GU 
       14.17        12.10        22.75        25.81         8.98         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD 
        0.26         2.10        12.95        23.84         9.67        27.42 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81         3.39         5.36         1.41         6.44         6.74 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        2.53         5.56        60.56         9.86        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-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        35.61         5.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       18.48        35.24        21.73         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91V 
       12.79         2.70        65.16        36.69        18.74        36.16 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O 
        9.50         9.73        52.24         9.04         4.54        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       42.54        11.24        22.09        32.94        29.98        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J 
       16.14        21.11 

$`4P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 
        7.43        18.35        30.90         6.18         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-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-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       21.11        30.90        32.94        12.82        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 
       15.42        28.01        15.32        12.43         3.45        12.76 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44        12.26        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 
       12.95         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        19.17         0.26        15.85 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        6.28         7.53        15.81        16.44        15.68         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56        13.87         6.08        13.41        13.51        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        12.82        19.36         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
       20.42         1.15        11.57         5.13         2.83        13.15 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       13.18         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         0.10         3.42         6.58         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 
        3.02        27.02        15.95         1.02        14.01        29.98 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
       21.99         0.00         9.01        12.00        22.98         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-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 
        7.99        12.36        12.66        11.93        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85        13.35        15.98        12.79        10.55 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        17.19        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.24        11.44         9.76         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34         7.13        16.24        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-HF-A5NB TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 
       13.58         0.56        18.08        14.27        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
        3.25        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 
       10.19        19.36        12.30         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR 
        3.45        18.38         5.19        13.08        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A93G TCGA-KB-A93H 
        5.56         1.81         7.82        13.51        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT 
        3.72        19.73         8.52        61.25         4.60         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        5.13       122.30        40.64       116.38        71.38        57.44 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       16.87        19.04         0.92        48.79        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK 
       32.48        28.96        34.29        16.31         2.50        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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       27.35        64.57        14.33        11.70        11.93        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 
       20.81        22.68         1.71         7.36         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 
        6.58         5.72        64.18         2.66        18.41        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       28.41        17.13        26.04        12.43        10.62         0.79 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.07              0.00 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           115.69            122.30 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           12.065            13.115 
[1] "0.1 - 115.7 (12.1)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         0        2       12       16        18        18
  4P LOSS WILD-TYPE       3       12       29       15        20        37
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           1         37         24         18       14
  4P LOSS WILD-TYPE         3         48         38         23       32
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 2                12
  STAGE IB                12                29
  STAGE II                16                15
  STAGE IIA               18                20
  STAGE IIB               18                37
  STAGE III                1                 3
  STAGE IIIA              37                48
  STAGE IIIB              24                38
  STAGE IIIC              18                23
  STAGE IV                14                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
  4P LOSS MUTATED     5  28  87  42
  4P LOSS WILD-TYPE  17  62 108  77
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               5                17
  T2              28                62
  T3              87               108
  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   43 41 40 34
  4P LOSS WILD-TYPE 86 77 44 55
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              43                86
  N1              41                77
  N2              40                44
  N3              34                55
[1] 4 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 237  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    150    7
  4P LOSS WILD-TYPE  237   23
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             150               237
  1               7                23
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    58 107
  4P LOSS WILD-TYPE 100 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     58  107
  4P LOSS WILD-TYPE  100  171
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              58               100
  MALE               107               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  4P LOSS MUTATED                                      21
  4P LOSS WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                       56
  4P LOSS WILD-TYPE                                                    106
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                                  37
  4P LOSS WILD-TYPE                                                                44
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  4P LOSS MUTATED                                                 34
  4P LOSS WILD-TYPE                                               44
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  4P LOSS MUTATED                                                          8
  4P LOSS WILD-TYPE                                                       13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  4P LOSS MUTATED                                                           2
  4P LOSS WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  4P LOSS MUTATED                                          7
  4P LOSS WILD-TYPE                                        6
D48V8, multiclass
                                                                   clus
vv                                                                  4P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         56
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        7
                                                                   clus
vv                                                                  4P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          106
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          6
[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"
D48V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     3 162
  4P LOSS WILD-TYPE   3 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3  162
  4P LOSS WILD-TYPE    3  268
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                3                 3
  YES             162               268
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED   129   7   6   8
  4P LOSS WILD-TYPE 218  11  13  17
D48V10, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0             129               218
  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"
D48V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED      37                         5
  4P LOSS WILD-TYPE    51                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           0    99
  4P LOSS WILD-TYPE                                         1   175
D48V12, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                                  37                51
  BLACK OR AFRICAN AMERICAN                               5                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  99               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"
D48V13, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1 116
  4P LOSS WILD-TYPE   3 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1  116
  4P LOSS WILD-TYPE    3  197
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO             116               197
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    90  61
  4Q LOSS WILD-TYPE 164  89
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              151               253 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               61                89 
$`4Q LOSS MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 
       11.01         9.44         6.61        17.29        19.33         9.17 
TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7959 
       31.20        35.24        18.15        28.73         9.07        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 
       17.49        14.43         0.69         9.60         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20        15.58         7.40        19.50        22.19        17.52 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
       14.04        14.79         3.72         5.39         9.21        20.22 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ 
        0.49        11.54         9.86        10.68         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
        1.48         0.72         0.66        13.51        20.65         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
       13.64         3.25         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 
        0.07         0.10         0.13         0.13         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 
       12.43        11.61        12.20        20.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 
       54.08         4.01        47.05        19.07        12.03        18.97 
TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6518 
       30.97        15.02        79.07         4.01        69.04        19.13 
TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
       20.55        17.19        10.26        15.22        15.98        11.31 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 
       19.50        18.21        16.44        11.31         7.40         0.62 
TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF TCGA-FP-A8CX 
        7.99        11.38        14.07        17.06         5.52         0.23 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GP 
        1.51         5.92        12.59        12.10        22.75         8.98 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
        6.25         0.26         2.10        12.95        23.84         9.67 
TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RP 
       27.42        18.81         3.39         5.36         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        6.74         5.56         2.53         9.86        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-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        35.61         5.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       18.48        35.24        21.73         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N 
       12.79         2.70        13.35        65.16        36.69        18.74 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O 
        9.50         9.73        52.24         9.04         4.54        21.04 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       42.54        22.09        29.98        54.12        16.14        21.11 
TCGA-VQ-AA6K 
       12.43 

$`4Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        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-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       23.93        15.42        28.01        15.32        12.43         3.45 
TCGA-BR-7958 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       12.76        11.44        12.26        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 
       12.95         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        19.17         0.26        15.85 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        6.28         7.53        15.81        16.44        15.68         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56        13.87         6.08        13.41        13.51        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        12.82        19.36         0.46 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
       20.42        11.57         5.13         2.83        13.15        13.18 
TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-A486 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        3.42         6.58         0.10        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 
       15.95         1.02        14.01        29.98        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        12.00        22.98         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-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       28.96        65.10        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       11.93        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       12.79        10.55        12.33        24.72        16.80        17.19 
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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO 
        2.96        15.65         8.38         4.34         7.13        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       14.47        72.23        21.27         3.48        19.53        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HJ-7597 
       59.54         5.03        13.58         0.56        18.08        26.47 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        14.17        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20         3.25        25.81 
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        10.19 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       19.36        12.30         8.88         8.81        21.21         3.45 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
       18.38         5.19        13.08        12.59         6.51         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
        7.82        13.51         5.56        60.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT 
        3.72        19.73         8.52        61.25         4.60         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        5.13       122.30        40.64       116.38        71.38        57.44 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       16.87        19.04         0.92        48.79        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK 
       32.48        28.96        34.29        16.31         2.50        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
        1.87         9.27        23.41        15.65        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       64.57        14.33        11.70        11.93        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 
       22.68         1.71        36.16         7.36         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        64.18         2.66        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 
       40.08        28.41        32.94        17.13        26.04        10.62 
TCGA-ZQ-A9CR 
        0.79 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.07              0.00 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           115.69            122.30 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            12.10             13.15 
[1] "0.1 - 115.7 (12.1)" "0.0 - 122.3 (13.2)"
[1] "hr=" "1.3"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         0        2       10       15        16        20
  4Q LOSS WILD-TYPE       3       12       31       16        22        35
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           2         36         24         18       15
  4Q LOSS WILD-TYPE         2         49         38         23       31
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 2                12
  STAGE IB                10                31
  STAGE II                15                16
  STAGE IIA               16                22
  STAGE IIB               20                35
  STAGE III                2                 2
  STAGE IIIA              36                49
  STAGE IIIB              24                38
  STAGE IIIC              18                23
  STAGE IV                15                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
  4Q LOSS MUTATED     4  30  81  44
  4Q LOSS WILD-TYPE  18  60 114  75
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               4                18
  T2              30                60
  T3              81               114
  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   39 45 38 34
  4Q LOSS WILD-TYPE 90 73 46 55
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              39                90
  N1              45                73
  N2              38                46
  N3              34                55
[1] 4 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   148   8
  4Q LOSS WILD-TYPE 239  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    148    8
  4Q LOSS WILD-TYPE  239   22
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             148               239
  1               8                22
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    61 101
  4Q LOSS WILD-TYPE  97 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     61  101
  4Q LOSS WILD-TYPE   97  177
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              61                97
  MALE               101               177
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  4Q LOSS MUTATED                                      20
  4Q LOSS WILD-TYPE                                    51
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                       55
  4Q LOSS WILD-TYPE                                                    107
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                                  38
  4Q LOSS WILD-TYPE                                                                43
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  4Q LOSS MUTATED                                                 32
  4Q LOSS WILD-TYPE                                               46
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  4Q LOSS MUTATED                                                          8
  4Q LOSS WILD-TYPE                                                       13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  4Q LOSS MUTATED                                                           2
  4Q LOSS WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  4Q LOSS MUTATED                                          7
  4Q LOSS WILD-TYPE                                        6
D49V8, multiclass
                                                                   clus
vv                                                                  4Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         55
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        7
                                                                   clus
vv                                                                  4Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          107
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 46
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          6
[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"
D49V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     3 159
  4Q LOSS WILD-TYPE   3 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3  159
  4Q LOSS WILD-TYPE    3  271
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                3                 3
  YES             159               271
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED   127   7   7   6
  4Q LOSS WILD-TYPE 220  11  12  19
D49V10, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             127               220
  R1               7                11
  R2               7                12
  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"
D49V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED      36                         5
  4Q LOSS WILD-TYPE    52                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           0   100
  4Q LOSS WILD-TYPE                                         1   174
D49V12, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                                  36                52
  BLACK OR AFRICAN AMERICAN                               5                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 100               174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     1 115
  4Q LOSS WILD-TYPE   3 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1  115
  4Q LOSS WILD-TYPE    3  198
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO             115               198
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    29  28
  5P LOSS WILD-TYPE 225 122
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               57               347 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28               122 
$`5P LOSS MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7958 
       11.01         9.44         6.61        19.33         9.17        12.76 
TCGA-BR-7959 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8683 TCGA-BR-8690 
       18.71         2.20        14.04         5.39         9.86        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4QI TCGA-CD-5800 
        7.53        22.26         1.48         0.72        13.64        13.15 
TCGA-CD-8535 TCGA-CD-A4MH TCGA-CG-4440 TCGA-CG-4449 TCGA-D7-6520 TCGA-D7-6815 
        0.13        12.20         4.01        19.07        18.84        15.98 
TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GH 
       72.23         0.56         5.52         5.92         0.76        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 
        8.98         6.25        23.84         9.67        21.21        18.81 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZF 
        5.19         6.44        60.56        37.64         9.86         8.52 
TCGA-R5-A7ZR TCGA-RD-A8MW TCGA-SW-A7EB TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PE 
        6.08        37.91         5.79        13.02         7.73        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PS TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A922 
       12.79         2.70        13.35         1.71         9.73         9.04 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-ZQ-A9CR 
       21.04        42.54         0.79 

$`5P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        19.50        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        19.17        14.79         0.26        15.85         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        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44        15.68         8.22        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        13.41        13.51        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        12.82         0.66        19.36        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        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        3.25        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58         0.10        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-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
       54.08        14.01        29.98        47.05        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
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-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
       12.66        11.93        19.13        20.55        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        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        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34         7.40         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        0.23        18.08        26.47         1.51        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        11.41        12.10        10.62        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        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        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        12.95        19.36        12.30         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       27.42         3.45         3.39        18.38         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        1.41         6.74        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A5UG 
        7.82        13.51         2.53         5.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       19.73        45.67        18.21        61.25         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67       122.30        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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK 
       28.96        34.29        46.26        16.31         2.50        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
        1.87         9.27        23.41        15.65        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        18.74        20.81        22.68        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.50        52.24         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
        5.72        64.18         2.66        11.24        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       40.08        28.41        32.94        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        21.11        12.43        10.62 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.13              0.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            72.23            122.30 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             9.86             13.25 
[1] "0.1 - 72.2 (9.9)"   "0.0 - 122.3 (13.2)"
[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        11
  5P LOSS WILD-TYPE       3       11       40       29        33        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           1         15          7          6        6
  5P LOSS WILD-TYPE         3         70         55         35       40
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 3                11
  STAGE IB                 1                40
  STAGE II                 2                29
  STAGE IIA                5                33
  STAGE IIB               11                44
  STAGE III                1                 3
  STAGE IIIA              15                70
  STAGE IIIB               7                55
  STAGE IIIC               6                35
  STAGE IV                 6                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
  5P LOSS MUTATED     4   8  25  20
  5P LOSS WILD-TYPE  18  82 170  99
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               4                18
  T2               8                82
  T3              25               170
  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
  5P LOSS MUTATED    11  20  12  12
  5P LOSS WILD-TYPE 118  98  72  77
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              11               118
  N1              20                98
  N2              12                72
  N3              12                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"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    53   4
  5P LOSS WILD-TYPE 334  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     53    4
  5P LOSS WILD-TYPE  334   26
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              53               334
  1               4                26
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    19  40
  5P LOSS WILD-TYPE 139 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     19   40
  5P LOSS WILD-TYPE  139  238
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              19               139
  MALE                40               238
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5P LOSS MUTATED                                       3
  5P LOSS WILD-TYPE                                    68
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                       21
  5P LOSS WILD-TYPE                                                    141
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                                  11
  5P LOSS WILD-TYPE                                                                70
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  5P LOSS MUTATED                                                 18
  5P LOSS WILD-TYPE                                               60
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5P LOSS MUTATED                                                          3
  5P LOSS WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  5P LOSS MUTATED                                                           1
  5P LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5P LOSS MUTATED                                          2
  5P LOSS WILD-TYPE                                       11
D50V8, multiclass
                                                                   clus
vv                                                                  5P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  5P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                70
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 60
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         11
[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"
D50V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  59
  5P LOSS WILD-TYPE   6 371
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   59
  5P LOSS WILD-TYPE    6  371
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                0                 6
  YES              59               371
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    45   2   4   3
  5P LOSS WILD-TYPE 302  16  15  22
D50V10, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              45               302
  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      15                         5
  5P LOSS WILD-TYPE    73                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           0    34
  5P LOSS WILD-TYPE                                         1   240
D50V12, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                                  15                73
  BLACK OR AFRICAN AMERICAN                               5                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  34               240
[1] 4 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  44
  5P LOSS WILD-TYPE   4 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   44
  5P LOSS WILD-TYPE    4  269
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              44               269
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    57  45
  5Q LOSS WILD-TYPE 197 105
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              102               302 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               45               105 
$`5Q LOSS MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 
       11.01         9.44         6.61        19.33         9.17         9.21 
TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8286 
       35.24        28.01         3.45        12.76        18.71        12.95 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8678 
        2.66         2.20        14.04        14.79         5.39        11.54 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.86         8.22        10.68         7.53        22.26         1.48 
TCGA-BR-A4J1 TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8526 
        0.72        13.64        13.15        13.18         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH 
        0.10         0.13         0.13        11.31        11.61        12.20 
TCGA-CG-4304 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-5718 TCGA-D7-5579 
       27.02         4.01        47.05        19.07        36.00        11.93 
TCGA-D7-6520 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-A6EX 
       18.84        10.26        15.98        12.79        12.33        11.31 
TCGA-D7-A6F0 TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
        2.96        72.23         0.56         5.52         5.92        12.59 
TCGA-HU-8610 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
        0.76         3.25        22.75        11.77         8.98         6.25 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RL 
       23.84         9.67        27.42        21.21        18.81         5.19 
TCGA-IN-A6RP TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZE 
        6.44         7.82        60.56        37.64         9.86        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU 
        8.52         6.08        37.91         8.94         5.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       13.25        13.02        35.24         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91U 
       12.79         2.70        17.85        13.35        27.35         1.71 
TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 
       36.16         9.73        52.24         9.04         2.01         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-ZQ-A9CR 
       21.04        42.54        40.08        32.94        17.13         0.79 

$`5Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        23.93        15.42        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.43         9.07        17.49        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       12.26         9.60        20.55         8.05         0.56        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        19.50        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-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       11.80        19.17         0.26        15.85         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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       15.68        12.56        13.87         6.08        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13         2.83         3.25         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.13         0.16         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         3.42         9.34        12.43         6.58         0.10 
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-4460 
        8.05        54.08        14.01        29.98        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
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-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        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        12.36        12.66 
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-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       17.19        15.22        10.55        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-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       13.71        11.24        11.44         9.76        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.99        16.24 
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-FP-A8CX 
       22.29        17.06        59.54         5.03        13.58         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       18.08        26.47         1.51        14.27        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10        10.62        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       24.20        25.81        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.88         8.81         3.45         3.39        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         1.41         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A5UG 
        1.81        13.51         2.53         5.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       19.73        45.67        61.25         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13        16.67       122.30        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-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        0.92        48.79        18.48        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM 
       32.48        28.96        34.29        16.31         2.50         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        26.24        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A927 
       20.81        22.68         7.36         9.50        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
        5.72        64.18         2.66        11.24        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        29.98        54.12        26.04        16.14        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        10.62 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.07              0.00 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            72.23            122.30 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           11.575            13.510 
[1] "0.1 - 72.2 (11.6)"  "0.0 - 122.3 (13.5)"
[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         7        15
  5Q LOSS WILD-TYPE       3       10       35       23        31        40
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           1         35         10         10        7
  5Q LOSS WILD-TYPE         3         50         52         31       39
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 4                10
  STAGE IB                 6                35
  STAGE II                 8                23
  STAGE IIA                7                31
  STAGE IIB               15                40
  STAGE III                1                 3
  STAGE IIIA              35                50
  STAGE IIIB              10                52
  STAGE IIIC              10                31
  STAGE IV                 7                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 LOSS MUTATED     5  18  50  30
  5Q LOSS WILD-TYPE  17  72 145  89
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               5                17
  T2              18                72
  T3              50               145
  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    24  35  24  18
  5Q LOSS WILD-TYPE 105  83  60  71
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              24               105
  N1              35                83
  N2              24                60
  N3              18                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"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    98   5
  5Q LOSS WILD-TYPE 289  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     98    5
  5Q LOSS WILD-TYPE  289   25
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              98               289
  1               5                25
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    37  68
  5Q LOSS WILD-TYPE 121 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     37   68
  5Q LOSS WILD-TYPE  121  210
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              37               121
  MALE                68               210
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5Q LOSS MUTATED                                       6
  5Q LOSS WILD-TYPE                                    65
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                       35
  5Q LOSS WILD-TYPE                                                    127
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                                  21
  5Q LOSS WILD-TYPE                                                                60
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  5Q LOSS MUTATED                                                 32
  5Q LOSS WILD-TYPE                                               46
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5Q LOSS MUTATED                                                          5
  5Q LOSS WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  5Q LOSS MUTATED                                                           3
  5Q LOSS WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5Q LOSS MUTATED                                          3
  5Q LOSS WILD-TYPE                                       10
D51V8, multiclass
                                                                   clus
vv                                                                  5Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         35
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  5Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 46
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         10
[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"
D51V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1 104
  5Q LOSS WILD-TYPE   5 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1  104
  5Q LOSS WILD-TYPE    5  326
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                1                 5
  YES             104               326
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    85   4   5   3
  5Q LOSS WILD-TYPE 262  14  14  22
D51V10, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              85               262
  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"
D51V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED      27                         5
  5Q LOSS WILD-TYPE    61                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           0    63
  5Q LOSS WILD-TYPE                                         1   211
D51V12, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                                  27                61
  BLACK OR AFRICAN AMERICAN                               5                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  63               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"
D51V13, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0  74
  5Q LOSS WILD-TYPE   4 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   74
  5Q LOSS WILD-TYPE    4  239
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              74               239
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    31  19
  6P LOSS WILD-TYPE 223 131
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               50               354 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19               131 
$`6P LOSS MUTATED`
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-7716 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 
        6.18        17.29        28.01        22.26         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A48A 
       20.65         1.15         0.16         0.10         0.13        12.43 
TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 
        1.02        12.03        15.02        12.66        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F2 
       18.54        13.35        15.98        11.24        11.31        15.65 
TCGA-F1-A72C TCGA-FP-8099 TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU 
       11.38        17.06        26.47        22.75        11.77         6.25 
TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU 
       12.95        27.42         5.19         6.44         5.56         1.81 
TCGA-MX-A663 TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N5 TCGA-VQ-A8DU TCGA-VQ-A8PU 
        9.86         6.08        16.67        57.44         5.46        27.35 
TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA6F TCGA-VQ-AA6I 
       14.33        20.81         9.04         4.54        54.12        16.14 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

$`6P LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        15.42        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        12.95         2.66        16.31         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        19.50        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        19.17        14.79         0.26        15.85         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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        12.56        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
       12.82         0.66        19.36         0.46        20.42        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.13         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        11.61         6.58        12.20         0.10 
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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       18.97         7.07        12.00        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 
       36.00         0.99         6.02         0.99       105.07        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       12.36        11.93        19.13        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        10.55        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-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.78        14.76        13.71        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34         7.40         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         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-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        5.52         0.23        18.08         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR 
        3.39        18.38         5.36        13.08         1.41         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         6.51         7.82        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 
       60.56        20.15        37.64         3.72        19.73        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52        61.25         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-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 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        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        26.24        64.57        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        11.93        61.22        18.74        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 
       36.16         7.36         9.50         9.73        52.24         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         6.58         5.72        64.18        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.54        11.24        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        29.98        17.13        26.04        21.11        12.43 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              0.1               0.0 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            57.44            122.30 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           12.545            12.855 
[1] "0.1 - 57.4 (12.5)"  "0.0 - 122.3 (12.9)"
[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        6        2         4         8
  6P LOSS WILD-TYPE       3       13       35       29        34        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           1         15          6          3        4
  6P LOSS WILD-TYPE         3         70         56         38       42
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 1                13
  STAGE IB                 6                35
  STAGE II                 2                29
  STAGE IIA                4                34
  STAGE IIB                8                47
  STAGE III                1                 3
  STAGE IIIA              15                70
  STAGE IIIB               6                56
  STAGE IIIC               3                38
  STAGE IV                 4                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
  6P LOSS MUTATED     2  14  28   8
  6P LOSS WILD-TYPE  20  76 167 111
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               2                20
  T2              14                76
  T3              28               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
  6P LOSS MUTATED    15  14  12   8
  6P LOSS WILD-TYPE 114 104  72  81
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              15               114
  N1              14               104
  N2              12                72
  N3               8                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    45   2
  6P LOSS WILD-TYPE 342  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     45    2
  6P LOSS WILD-TYPE  342   28
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              45               342
  1               2                28
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    17  35
  6P LOSS WILD-TYPE 141 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     17   35
  6P LOSS WILD-TYPE  141  243
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              17               141
  MALE                35               243
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6P LOSS MUTATED                                       7
  6P LOSS WILD-TYPE                                    64
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                       21
  6P LOSS WILD-TYPE                                                    141
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                                   5
  6P LOSS WILD-TYPE                                                                76
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  6P LOSS MUTATED                                                 17
  6P LOSS WILD-TYPE                                               61
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6P LOSS MUTATED                                                          1
  6P LOSS WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  6P LOSS MUTATED                                                           0
  6P LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6P LOSS MUTATED                                          1
  6P LOSS WILD-TYPE                                       12
D52V8, multiclass
                                                                   clus
vv                                                                  6P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  6P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                76
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         12
[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"
D52V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0  52
  6P LOSS WILD-TYPE   6 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   52
  6P LOSS WILD-TYPE    6  378
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                0                 6
  YES              52               378
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    45   0   2   3
  6P LOSS WILD-TYPE 302  18  17  22
D52V10, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              45               302
  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                         1
  6P LOSS WILD-TYPE    77                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           0    35
  6P LOSS WILD-TYPE                                         1   239
D52V12, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               1                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  35               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"
D52V13, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0  41
  6P LOSS WILD-TYPE   4 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   41
  6P LOSS WILD-TYPE    4  272
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              41               272
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    38  26
  6Q LOSS WILD-TYPE 216 124
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               64               340 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               26               124 
$`6Q LOSS MUTATED`
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-8080 
        6.18        17.29         9.17        28.01        15.32         9.60 
TCGA-BR-A4CQ TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5803 TCGA-CD-8530 
       22.26        13.51        20.65         1.15         0.07         0.16 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A48A TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-5719 
        0.10         0.13        12.43        29.98        12.03         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.03        15.02        12.66        20.55        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EV TCGA-D7-A6EX 
       13.35        15.98        24.72        14.66        11.24        11.31 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       15.65         7.40        11.38        17.06        13.58         0.56 
TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RL 
       26.47        22.75         6.25        23.84        27.42         5.19 
TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        6.44         5.56         1.81         9.86        18.21         6.08 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-VQ-A8DU TCGA-VQ-A8PS TCGA-VQ-A8PU 
       16.67       122.30        57.44         5.46        13.35        27.35 
TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O 
       14.33        20.81         9.04         2.01         4.54        21.04 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        16.14        10.62         0.79 

$`6Q LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       15.42        18.15        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       12.26        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        13.41        13.51        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        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36         0.46        20.42        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
        0.13         0.10         3.42         9.34        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         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
        4.01        14.01        47.05        19.07        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 
        7.99        12.36        11.93        19.13        18.61        17.85 
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        10.55        11.31 
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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       14.76        13.71        11.44         9.76         2.96         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        4.34         7.13         0.62         7.99        16.24        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-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 
       59.54         5.03         5.52         0.23        18.08         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
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        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
       13.08         1.41         6.74        12.59         6.51         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
       13.51         2.53         5.56        60.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
        3.72        19.73        45.67         8.52        61.25         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 
        9.24        11.05         8.61         5.13        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        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        28.96        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-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       23.41        15.65        26.24        64.57        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        11.93        61.22        18.74        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 
       36.16         7.36         9.50         9.73        52.24        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58         5.72        64.18         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       22.09        18.41        40.08        28.41        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        26.04        21.11        12.43 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.00 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           122.30            116.38 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           13.350            12.805 
[1] "0.1 - 122.3 (13.3)" "0.0 - 116.4 (12.8)"
[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        6        4         4        12
  6Q LOSS WILD-TYPE       3       13       35       27        34        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           1         20          8          6        4
  6Q LOSS WILD-TYPE         3         65         54         35       42
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 1                13
  STAGE IB                 6                35
  STAGE II                 4                27
  STAGE IIA                4                34
  STAGE IIB               12                43
  STAGE III                1                 3
  STAGE IIIA              20                65
  STAGE IIIB               8                54
  STAGE IIIC               6                35
  STAGE IV                 4                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
  6Q LOSS MUTATED     2  16  39  11
  6Q LOSS WILD-TYPE  20  74 156 108
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               2                20
  T2              16                74
  T3              39               156
  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
  6Q LOSS MUTATED    17  20  17  12
  6Q LOSS WILD-TYPE 112  98  67  77
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              17               112
  N1              20                98
  N2              17                67
  N3              12                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"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    60   2
  6Q LOSS WILD-TYPE 327  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     60    2
  6Q LOSS WILD-TYPE  327   28
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              60               327
  1               2                28
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    22  47
  6Q LOSS WILD-TYPE 136 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     22   47
  6Q LOSS WILD-TYPE  136  231
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              22               136
  MALE                47               231
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6Q LOSS MUTATED                                       8
  6Q LOSS WILD-TYPE                                    63
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                       26
  6Q LOSS WILD-TYPE                                                    136
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                                  10
  6Q LOSS WILD-TYPE                                                                71
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  6Q LOSS MUTATED                                                 21
  6Q LOSS WILD-TYPE                                               57
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6Q LOSS MUTATED                                                          3
  6Q LOSS WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  6Q LOSS MUTATED                                                           0
  6Q LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6Q LOSS MUTATED                                          1
  6Q LOSS WILD-TYPE                                       12
D53V8, multiclass
                                                                   clus
vv                                                                  6Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  6Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          136
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                71
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         12
[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"
D53V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0  69
  6Q LOSS WILD-TYPE   6 361
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   69
  6Q LOSS WILD-TYPE    6  361
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                0                 6
  YES              69               361
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    58   1   2   4
  6Q LOSS WILD-TYPE 289  17  17  21
D53V10, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              58               289
  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                         2
  6Q LOSS WILD-TYPE    77                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           0    48
  6Q LOSS WILD-TYPE                                         1   226
D53V12, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  48               226
[1] 4 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  52
  6Q LOSS WILD-TYPE   4 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   52
  6Q LOSS WILD-TYPE    4  261
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              52               261
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    13   6
  7P LOSS WILD-TYPE 241 144
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               19               385 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6               144 
$`7P LOSS MUTATED`
TCGA-BR-7723 TCGA-BR-8678 TCGA-CG-4438 TCGA-CG-4443 TCGA-D7-6820 TCGA-D7-8573 
       28.73        11.54        54.08        29.98        11.31        19.50 
TCGA-D7-A6EX TCGA-FP-8631 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-IN-A6RN TCGA-IN-A7NU 
       11.31         0.56        11.77         6.25        13.08         1.81 
TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PJ 
       37.91        35.61         5.46        13.02        18.48         2.70 
TCGA-VQ-A91S 
       22.68 

$`7P LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
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        19.50        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        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        12.82         0.66        19.36 
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        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        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         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
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-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        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-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        10.55        12.33        24.72        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-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.44         9.76         2.96        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.99        16.24 
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-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        5.52         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       27.42        21.21         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19         1.41         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51         5.56         7.82        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
       60.56        20.15        37.64         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        61.25         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-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-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        16.31        22.19         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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       13.35        26.24        27.35        64.57        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       36.69        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        36.16         7.36         9.50         9.73        52.24 
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-A94U 
       64.18        21.04         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        40.08        28.41        32.94        29.98        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        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        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 
            13.02             12.82 
[1] "0.6 - 54.1 (13.0)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
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       3       12       40       30        37        53
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           0          5          3          2        3
  7P LOSS WILD-TYPE         4         80         59         39       43
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 2                12
  STAGE IB                 1                40
  STAGE II                 1                30
  STAGE IIA                1                37
  STAGE IIB                2                53
  STAGE III                0                 4
  STAGE IIIA               5                80
  STAGE IIIB               3                59
  STAGE IIIC               2                39
  STAGE IV                 3                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
  7P LOSS MUTATED     3   3  10   4
  7P LOSS WILD-TYPE  19  87 185 115
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               3                19
  T2               3                87
  T3              10               185
  T4               4               115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P LOSS MUTATED     4   5   7   4
  7P LOSS WILD-TYPE 125 113  77  85
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               4               125
  N1               5               113
  N2               7                77
  N3               4                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"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    17   2
  7P LOSS WILD-TYPE 370  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     17    2
  7P LOSS WILD-TYPE  370   28
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              17               370
  1               2                28
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     4  16
  7P LOSS WILD-TYPE 154 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      4   16
  7P LOSS WILD-TYPE  154  262
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               4               154
  MALE                16               262
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7P LOSS MUTATED                                       2
  7P LOSS WILD-TYPE                                    69
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                        6
  7P LOSS WILD-TYPE                                                    156
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                                   5
  7P LOSS WILD-TYPE                                                                76
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  7P LOSS MUTATED                                                  6
  7P LOSS WILD-TYPE                                               72
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7P LOSS MUTATED                                                          0
  7P LOSS WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  7P LOSS MUTATED                                                           0
  7P LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7P LOSS MUTATED                                          1
  7P LOSS WILD-TYPE                                       12
D54V8, multiclass
                                                                   clus
vv                                                                  7P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  7P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            69
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                76
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 72
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         12
[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"
D54V9, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  20
  7P LOSS WILD-TYPE   6 410
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   20
  7P LOSS WILD-TYPE    6  410
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                 6
  YES              20               410
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    17   0   2   1
  7P LOSS WILD-TYPE 330  18  17  24
D54V10, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              17               330
  R1               0                18
  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"
D54V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED       3                         3
  7P LOSS WILD-TYPE    85                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           0    11
  7P LOSS WILD-TYPE                                         1   263
D54V12, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                                   3                85
  BLACK OR AFRICAN AMERICAN                               3                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               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"
D54V13, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  13
  7P LOSS WILD-TYPE   4 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   13
  7P LOSS WILD-TYPE    4  300
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              13               300
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    18   9
  7Q LOSS WILD-TYPE 236 141
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               27               377 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                9               141 
$`7Q LOSS MUTATED`
TCGA-BR-7723 TCGA-BR-8369 TCGA-BR-8678 TCGA-BR-A4CS TCGA-CD-A48C TCGA-CG-4438 
       28.73        14.04        11.54         1.48        11.61        54.08 
TCGA-CG-4443 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EX TCGA-FP-7829 TCGA-FP-8631 
       29.98        11.31        18.21        11.31        19.53         0.56 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI 
       22.75        11.77         6.25         9.67        27.42        18.38 
TCGA-IN-A6RN TCGA-IN-A7NU TCGA-KB-A93H TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-VQ-A8DU 
       13.08         1.81        37.64        37.91        35.61         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PJ 
       13.02        18.48         2.70 

$`7Q LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
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        19.50        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-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        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        12.82         0.66        19.36        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        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42         9.34        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 
        0.10        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-4444 
        1.02         7.99         8.05         4.01        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        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        12.36        12.66        11.93        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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
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-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        2.96        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         5.52         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20         3.25        25.81        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        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        23.84        12.30         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21         3.45        18.81         3.39         5.36         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        1.41         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73         9.86        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67       122.30        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-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        0.92        48.79        13.25        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        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-A8PU 
        9.27        23.41        15.65        13.35        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        7.36         9.50         9.73        52.24         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        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
        2.66        42.54        11.24        22.09        18.41        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        32.94        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         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 
            13.08             12.79 
[1] "0.6 - 54.1 (13.1)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         1        2        1        2         1         6
  7Q LOSS WILD-TYPE       2       12       40       29        37        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           0          8          3          3        3
  7Q LOSS WILD-TYPE         4         77         59         38       43
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 2                12
  STAGE IB                 1                40
  STAGE II                 2                29
  STAGE IIA                1                37
  STAGE IIB                6                49
  STAGE III                0                 4
  STAGE IIIA               8                77
  STAGE IIIB               3                59
  STAGE IIIC               3                38
  STAGE IV                 3                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
  7Q LOSS MUTATED     4   3  19   4
  7Q LOSS WILD-TYPE  18  87 176 115
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               4                18
  T2               3                87
  T3              19               176
  T4               4               115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q LOSS MUTATED     6   8  10   6
  7Q LOSS WILD-TYPE 123 110  74  83
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               6               123
  N1               8               110
  N2              10                74
  N3               6                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"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    27   2
  7Q LOSS WILD-TYPE 360  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     27    2
  7Q LOSS WILD-TYPE  360   28
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              27               360
  1               2                28
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     8  22
  7Q LOSS WILD-TYPE 150 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      8   22
  7Q LOSS WILD-TYPE  150  256
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               8               150
  MALE                22               256
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7Q LOSS MUTATED                                       3
  7Q LOSS WILD-TYPE                                    68
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                       11
  7Q LOSS WILD-TYPE                                                    151
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                                   5
  7Q LOSS WILD-TYPE                                                                76
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  7Q LOSS MUTATED                                                  9
  7Q LOSS WILD-TYPE                                               69
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7Q LOSS MUTATED                                                          1
  7Q LOSS WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  7Q LOSS MUTATED                                                           0
  7Q LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7Q LOSS MUTATED                                          1
  7Q LOSS WILD-TYPE                                       12
D55V8, multiclass
                                                                   clus
vv                                                                  7Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  7Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                76
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 69
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         12
[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"
D55V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  30
  7Q LOSS WILD-TYPE   6 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   30
  7Q LOSS WILD-TYPE    6  400
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                 6
  YES              30               400
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    26   0   2   1
  7Q LOSS WILD-TYPE 321  18  17  24
D55V10, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              26               321
  R1               0                18
  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"
D55V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED       9                         2
  7Q LOSS WILD-TYPE    79                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           0    16
  7Q LOSS WILD-TYPE                                         1   258
D55V12, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                                   9                79
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  16               258
[1] 4 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   4 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   23
  7Q LOSS WILD-TYPE    4  290
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              23               290
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    45  36
  8P LOSS WILD-TYPE 209 114
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               81               323 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               36               114 
$`8P LOSS MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6705 TCGA-BR-6709 
       19.56         9.44        18.35        17.29        25.61        12.16 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8296 
       28.01        28.73        12.76         0.69        12.95        15.58 
TCGA-BR-8362 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4IY 
       13.08        15.81         9.86         8.22        13.87        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8526 TCGA-CD-8533 
        0.72        13.51         1.15        13.64         0.07         0.13 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       11.61        12.20         3.02         7.99        54.08         4.01 
TCGA-CG-4449 TCGA-CG-4475 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6521 
       19.07        22.98        12.03         4.01        69.04        18.54 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6F2 
       10.26        15.22        24.72        18.21        16.44        15.65 
TCGA-D7-A74A TCGA-FP-8099 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GU 
        7.40        17.06         5.92        14.17         0.76         6.25 
TCGA-HU-A4HD TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V 
       27.42         1.41         6.44         6.74         1.81         7.82 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-R5-A7O7 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV 
        2.53         5.56        45.67         9.24         8.61       122.30 
TCGA-RD-A8MW TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
       37.91        18.48        35.24        34.45         7.73        46.26 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Z 
       17.85         1.87        13.35        20.81         1.71        52.24 
TCGA-VQ-A925 TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F 
        4.54        11.24        18.41        40.08        29.98        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       16.14        21.11        12.43 

$`8P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        30.90         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-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
       24.76        35.24        23.93        15.42        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45         9.07        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        16.31         2.20         7.40         6.18        19.50 
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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 
        7.53         0.49        11.54        16.44        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51         8.98        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36         0.46        20.65        20.42        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        12.43         6.58         0.10        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       27.02        15.95         1.02         8.05        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        12.03        21.99         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-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       79.07        65.10        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        20.55        18.84        18.61        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        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       12.33        16.80        19.50        17.19        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        8.38         4.34         7.13         0.62         7.99        16.24 
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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
        5.52         0.23        18.08        26.47         1.51        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       12.59        11.41        12.10        10.62        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        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 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88         8.81        21.21         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         5.36         5.19        13.08 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G 
       12.59         6.51         5.56        13.51        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       37.64         3.72        19.73         9.86        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       61.25         6.08         4.60        11.05         5.13        16.67 
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-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        13.25        13.02        21.73        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
        2.70         9.27        23.41        15.65        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        18.74        22.68        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA69 
       64.18        21.04         2.66        42.54        22.09        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       32.94        17.13        26.04        10.62         0.79 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.07              0.00 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           122.30            116.38 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            13.35             12.79 
[1] "0.1 - 122.3 (13.3)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.2"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         1        3        3        4         4         8
  8P LOSS WILD-TYPE       2       11       38       27        34        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           0         17         21         10       12
  8P LOSS WILD-TYPE         4         68         41         31       34
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 3                11
  STAGE IB                 3                38
  STAGE II                 4                27
  STAGE IIA                4                34
  STAGE IIB                8                47
  STAGE III                0                 4
  STAGE IIIA              17                68
  STAGE IIIB              21                41
  STAGE IIIC              10                31
  STAGE IV                12                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
  8P LOSS MUTATED     5   9  50  20
  8P LOSS WILD-TYPE  17  81 145  99
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               5                17
  T2               9                81
  T3              50               145
  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
  8P LOSS MUTATED    14  23  23  23
  8P LOSS WILD-TYPE 115  95  61  66
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              14               115
  N1              23                95
  N2              23                61
  N3              23                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"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    75   7
  8P LOSS WILD-TYPE 312  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     75    7
  8P LOSS WILD-TYPE  312   23
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              75               312
  1               7                23
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    20  65
  8P LOSS WILD-TYPE 138 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     20   65
  8P LOSS WILD-TYPE  138  213
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              20               138
  MALE                65               213
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8P LOSS MUTATED                                       5
  8P LOSS WILD-TYPE                                    66
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                       31
  8P LOSS WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                                  23
  8P LOSS WILD-TYPE                                                                58
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  8P LOSS MUTATED                                                 20
  8P LOSS WILD-TYPE                                               58
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8P LOSS MUTATED                                                          1
  8P LOSS WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  8P LOSS MUTATED                                                           1
  8P LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8P LOSS MUTATED                                          3
  8P LOSS WILD-TYPE                                       10
D56V8, multiclass
                                                                   clus
vv                                                                  8P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  8P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         10
[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"
D56V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1  84
  8P LOSS WILD-TYPE   5 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   84
  8P LOSS WILD-TYPE    5  346
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                1                 5
  YES              84               346
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED    67   4   6   2
  8P LOSS WILD-TYPE 280  14  13  23
D56V10, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              67               280
  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                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           1    52
  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                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  52               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     1  53
  8P LOSS WILD-TYPE   3 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   53
  8P LOSS WILD-TYPE    3  260
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              53               260
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    16  16
  8Q LOSS WILD-TYPE 238 134
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               32               372 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               16               134 
$`8Q LOSS MUTATED`
TCGA-BR-4191 TCGA-BR-6705 TCGA-BR-8286 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-A48C 
       18.35        25.61        12.95        13.51        13.64        11.61 
TCGA-CD-A4MH TCGA-CG-4440 TCGA-CG-4475 TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6527 
       12.20         4.01        22.98        12.03        18.54        10.26 
TCGA-D7-8570 TCGA-FP-8099 TCGA-HU-8249 TCGA-IN-A7NU TCGA-IN-AB1V TCGA-R5-A805 
       24.72        17.06        14.17         1.81         7.82         9.24 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PM 
        8.61       122.30        18.48        34.45        17.85         1.87 
TCGA-VQ-A8PY TCGA-VQ-A91U TCGA-VQ-A925 TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6F 
       14.33         1.71         4.54        11.24        29.98        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J 
       16.14        21.11 

$`8Q LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
        6.61         6.97         4.64         7.43        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        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-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        16.31         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        19.50        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        19.17        14.79         0.26        15.85         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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        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        12.82         0.66        19.36         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        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        11.31        12.43         6.58         0.10        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-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.08        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         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-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        11.93        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        12.33        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        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44         9.76         2.96        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.99        16.24 
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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        5.52         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       14.27        12.59        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.81        27.42        21.21         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.38         5.36         5.19        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-IP-7968 
        6.74        12.59         6.51         5.56        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        9.86        45.67        18.21         8.52        61.25         6.08 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
        4.60        11.05         5.13        16.67        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-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        35.24        21.73        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        28.96        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        26.24        27.35        64.57        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       36.16         7.36         9.50         9.73        52.24         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        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       32.94        17.13        26.04        12.43        10.62         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 
           13.905            12.790 
[1] "1.7 - 122.3 (13.9)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.3"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         0        1        0        2         3         3
  8Q LOSS WILD-TYPE       3       13       41       29        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           0          6         10          1        5
  8Q LOSS WILD-TYPE         4         79         52         40       41
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  0                 3
  STAGE IA                 1                13
  STAGE IB                 0                41
  STAGE II                 2                29
  STAGE IIA                3                35
  STAGE IIB                3                52
  STAGE III                0                 4
  STAGE IIIA               6                79
  STAGE IIIB              10                52
  STAGE IIIC               1                40
  STAGE IV                 5                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
  8Q LOSS MUTATED     1   3  26   2
  8Q LOSS WILD-TYPE  21  87 169 117
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               1                21
  T2               3                87
  T3              26               169
  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     5   7  10  10
  8Q LOSS WILD-TYPE 124 111  74  79
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               5               124
  N1               7               111
  N2              10                74
  N3              10                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    29   3
  8Q LOSS WILD-TYPE 358  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     29    3
  8Q LOSS WILD-TYPE  358   27
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              29               358
  1               3                27
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     7  26
  8Q LOSS WILD-TYPE 151 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7   26
  8Q LOSS WILD-TYPE  151  252
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               7               151
  MALE                26               252
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8Q LOSS MUTATED                                       3
  8Q LOSS WILD-TYPE                                    68
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                       10
  8Q LOSS WILD-TYPE                                                    152
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                                  11
  8Q LOSS WILD-TYPE                                                                70
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  8Q LOSS MUTATED                                                  6
  8Q LOSS WILD-TYPE                                               72
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8Q LOSS MUTATED                                                          0
  8Q LOSS WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  8Q LOSS MUTATED                                                           1
  8Q LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8Q LOSS MUTATED                                          1
  8Q LOSS WILD-TYPE                                       12
D57V8, multiclass
                                                                   clus
vv                                                                  8Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  8Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                70
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 72
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         12
[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"
D57V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  33
  8Q LOSS WILD-TYPE   6 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   33
  8Q LOSS WILD-TYPE    6  397
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 6
  YES              33               397
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    24   0   4   2
  8Q LOSS WILD-TYPE 323  18  15  23
D57V10, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              24               323
  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       4                         2
  8Q LOSS WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           1    22
  8Q LOSS WILD-TYPE                                         0   252
D57V12, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                                   4                84
  BLACK OR AFRICAN AMERICAN                               2                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  22               252
[1] 4 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  18
  8Q LOSS WILD-TYPE   4 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   18
  8Q LOSS WILD-TYPE    4  295
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              18               295
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    81  55
  9P LOSS WILD-TYPE 173  95
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              136               268 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               55                95 
$`9P LOSS MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6803 
       11.01         9.44        18.35        13.68        19.33        31.20 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 
        9.21        35.24        28.01        28.73         3.45        17.49 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 
       11.44         0.69        12.95        16.31        22.19        17.52 
TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8683 
       14.04         5.39        25.18         9.21        20.22         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       15.68         8.22        13.87        22.26         1.48         0.72 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 
        0.66        13.51        20.65         1.15         3.25        13.15 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8532 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 
        0.13         3.42        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        11.93 
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-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU 
       15.98        12.79        18.21        14.66        21.14        16.44 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 
       11.24        11.31         2.96         7.40         7.99        72.23 
TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 
       11.38        17.06         0.56         1.51         5.92        12.59 
TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       11.77         6.25         9.67        27.42        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT 
       18.38         5.36         1.41         6.74         6.51         5.56 
TCGA-IN-AB1V TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 
        7.82        37.64        45.67         8.52         6.08         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
        8.61         5.13        16.67        37.91         8.94         5.79 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE 
       13.25        18.48        35.24        34.45         7.73        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PY 
       12.79         2.70        17.85         1.87        27.35        14.33 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        20.81         1.71        36.16         9.50         9.73 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04        42.54        11.24        22.09        18.41        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       32.94        21.11        12.43         0.79 

$`9P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        19.56         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        17.29        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-6852 TCGA-BR-7196 TCGA-BR-7703 
        8.98        21.11        30.90        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 
       23.93        15.42        18.15        15.32        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       12.76        18.71        14.43        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56         2.66         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        13.08         0.26         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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       15.85         3.72         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
       16.44        10.68        12.56         7.53         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         8.98        14.17         0.53        12.82 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36         0.46        20.42        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        2.83        13.18         0.30         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         0.10         9.34        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
        6.58        12.20         0.10        12.62        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4444 
       15.95         1.02         7.99         8.05        14.01        47.05 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       21.99         0.00         9.01         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        6.97         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        79.07        65.10        21.07         7.99        12.36 
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        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 
       12.33        24.72        16.80        19.50        17.19        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44         9.76        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        0.62        16.24        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-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
        0.23        18.08        26.47        14.27        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        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        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        2.10        12.95        19.36        23.84        12.30         8.88 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        8.81         3.45         3.39         5.19        13.08         6.44 
TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       12.59         1.81        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI 
       20.15         3.72        19.73         9.86        18.21        61.25 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        4.60        11.05       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44        35.61        16.87        19.04         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       48.79         5.46        13.02        21.73        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO 
       28.96        34.29        46.26        16.31         2.50         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        26.24        64.57        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W 
       36.69        11.70        11.93        61.22        22.68         7.36 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       52.24         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
        5.72        64.18         2.66        28.41        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       54.12        26.04        16.14        10.62 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.00 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            72.23            122.30 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           12.725            12.920 
[1] "0.1 - 72.2 (12.7)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.2"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         1        6       10       15        10        17
  9P LOSS WILD-TYPE       2        8       31       16        28        38
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           1         29         23         12       18
  9P LOSS WILD-TYPE         3         56         39         29       28
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 6                 8
  STAGE IB                10                31
  STAGE II                15                16
  STAGE IIA               10                28
  STAGE IIB               17                38
  STAGE III                1                 3
  STAGE IIIA              29                56
  STAGE IIIB              23                39
  STAGE IIIC              12                29
  STAGE IV                18                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
  9P LOSS MUTATED     7  29  71  35
  9P LOSS WILD-TYPE  15  61 124  84
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               7                15
  T2              29                61
  T3              71               124
  T4              35                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"
                   vv
clus                N0 N1 N2 N3
  9P LOSS MUTATED   39 37 37 28
  9P LOSS WILD-TYPE 90 81 47 61
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              39                90
  N1              37                81
  N2              37                47
  N3              28                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"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   132   9
  9P LOSS WILD-TYPE 255  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    132    9
  9P LOSS WILD-TYPE  255   21
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             132               255
  1               9                21
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    56  90
  9P LOSS WILD-TYPE 102 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     56   90
  9P LOSS WILD-TYPE  102  188
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              56               102
  MALE                90               188
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9P LOSS MUTATED                                      13
  9P LOSS WILD-TYPE                                    58
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                       52
  9P LOSS WILD-TYPE                                                    110
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                                  35
  9P LOSS WILD-TYPE                                                                46
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  9P LOSS MUTATED                                                 33
  9P LOSS WILD-TYPE                                               45
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9P LOSS MUTATED                                                          6
  9P LOSS WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  9P LOSS MUTATED                                                           3
  9P LOSS WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9P LOSS MUTATED                                          3
  9P LOSS WILD-TYPE                                       10
D58V8, multiclass
                                                                   clus
vv                                                                  9P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  9P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          110
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         10
[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"
D58V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     3 143
  9P LOSS WILD-TYPE   3 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3  143
  9P LOSS WILD-TYPE    3  287
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                3                 3
  YES             143               287
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED   119   5   6   5
  9P LOSS WILD-TYPE 228  13  13  20
D58V10, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             119               228
  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                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           1    91
  9P LOSS WILD-TYPE                                         0   183
D58V12, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                                  27                61
  BLACK OR AFRICAN AMERICAN                               6                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  91               183
[1] 4 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     1 101
  9P LOSS WILD-TYPE   3 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1  101
  9P LOSS WILD-TYPE    3  212
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO             101               212
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    56  36
  9Q LOSS WILD-TYPE 198 114
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               92               312 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               36               114 
$`9Q LOSS MUTATED`
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 
       13.68        19.33        31.20         9.21        28.01        28.73 
TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8364 
        3.45        17.49        11.44        12.95        16.31        22.19 
TCGA-BR-8365 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8686 TCGA-BR-A44U 
       17.52         5.39        25.18         9.21        15.68        13.87 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5803 
        1.48         0.72        13.51         1.15         3.25         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 
        0.07         0.07         0.07         0.10         0.13         3.42 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       11.61        12.20         3.02        54.08         4.01        29.98 
TCGA-CG-4455 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6527 
       12.03        20.55        18.84        18.54        13.35        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU 
       15.98        12.79        18.21        14.66        21.14        16.44 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 
        2.96         7.40         7.99        72.23        11.38        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 
       13.58         0.56         5.92        11.77         6.25         2.10 
TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V 
       27.42        18.38         5.36         6.74         6.51         7.82 
TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MW 
       37.64        45.67         8.52         6.08        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        35.24        34.45 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91Q 
       22.19        12.79         2.70        17.85        13.35        20.81 
TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA68 
        1.71         9.73        21.04        42.54        22.09        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6J 
       32.94        21.11 

$`9Q LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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        21.11        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82        24.76        35.24        23.93        15.42 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        12.43         9.07        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.56         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 
       19.50        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       15.85         3.72        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44         9.86         8.22        10.68        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        22.26        13.41        13.51        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        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65        20.42        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8526 TCGA-CD-8528 
        2.83        13.15        13.18         0.30         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
        0.13         0.16         0.10         0.13         0.10         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        12.43         6.58         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        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        12.36        12.66        11.93        19.13 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 
       18.61        17.85        17.19        15.22        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 
       12.33        24.72        16.80        19.50        17.19        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44         9.76        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 
        4.34         7.13         0.62        16.24        14.47        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        59.54         5.03 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
        5.52         0.23        18.08        26.47         1.51        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51        10.19         0.26        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.81         3.39         5.19        13.08         1.41         6.44 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         5.56         1.81        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE 
       60.56        20.15         3.72        19.73         9.86        18.21 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       61.25         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        27.88        32.48         7.73        28.96 
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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       22.68        36.16         7.36         9.50        52.24         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        64.18 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
        2.66        11.24        18.41        28.41        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        12.43        10.62         0.79 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            72.23            122.30 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           13.300            12.775 
[1] "0.1 - 72.2 (13.3)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         1        4        7       11         8        12
  9Q LOSS WILD-TYPE       2       10       34       20        30        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           1         19         15         10       11
  9Q LOSS WILD-TYPE         3         66         47         31       35
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 4                10
  STAGE IB                 7                34
  STAGE II                11                20
  STAGE IIA                8                30
  STAGE IIB               12                43
  STAGE III                1                 3
  STAGE IIIA              19                66
  STAGE IIIB              15                47
  STAGE IIIC              10                31
  STAGE IV                11                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
  9Q LOSS MUTATED     5  20  52  22
  9Q LOSS WILD-TYPE  17  70 143  97
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               5                17
  T2              20                70
  T3              52               143
  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
  9Q LOSS MUTATED    28  27  22  22
  9Q LOSS WILD-TYPE 101  91  62  67
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              28               101
  N1              27                91
  N2              22                62
  N3              22                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"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    90   7
  9Q LOSS WILD-TYPE 297  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     90    7
  9Q LOSS WILD-TYPE  297   23
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              90               297
  1               7                23
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    34  68
  9Q LOSS WILD-TYPE 124 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     34   68
  9Q LOSS WILD-TYPE  124  210
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              34               124
  MALE                68               210
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9Q LOSS MUTATED                                      11
  9Q LOSS WILD-TYPE                                    60
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                       40
  9Q LOSS WILD-TYPE                                                    122
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                                  22
  9Q LOSS WILD-TYPE                                                                59
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  9Q LOSS MUTATED                                                 23
  9Q LOSS WILD-TYPE                                               55
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9Q LOSS MUTATED                                                          4
  9Q LOSS WILD-TYPE                                                       17
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  9Q LOSS MUTATED                                                           1
  9Q LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9Q LOSS MUTATED                                          1
  9Q LOSS WILD-TYPE                                       12
D59V8, multiclass
                                                                   clus
vv                                                                  9Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  9Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         12
[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"
D59V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     3  99
  9Q LOSS WILD-TYPE   3 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3   99
  9Q LOSS WILD-TYPE    3  331
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                3                 3
  YES              99               331
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    82   3   4   4
  9Q LOSS WILD-TYPE 265  15  15  21
D59V10, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              82               265
  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      22                         6
  9Q LOSS WILD-TYPE    66                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           0    64
  9Q LOSS WILD-TYPE                                         1   210
D59V12, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                                  22                66
  BLACK OR AFRICAN AMERICAN                               6                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  64               210
[1] 4 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  74
  9Q LOSS WILD-TYPE   3 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   74
  9Q LOSS WILD-TYPE    3  239
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              74               239
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    30  29
  10P LOSS WILD-TYPE 224 121
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                59                345 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                29                121 
$`10P LOSS MUTATED`
TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7901 
       19.56        18.35         6.18        19.33        26.10         3.45 
TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4IY 
       11.44        16.31        17.52        20.22         7.53        12.89 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8533 TCGA-CG-4436 TCGA-CG-4455 
        0.07         0.07         0.10         0.13         7.99        12.03 
TCGA-CG-4475 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       22.98        69.04        18.54        10.26        15.22        15.98 
TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EV TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8631 
       11.31        18.21        11.24         7.99        19.53         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8249 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RO 
        5.52         0.23        14.17        18.81        18.38         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-RD-A8N1 TCGA-RD-A8N6 
        6.44         6.74        45.67         8.52       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE 
        5.79        48.79        13.02        18.48        35.24        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A928 
       17.85        13.35        36.69        18.74        20.81         5.72 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       11.24        18.41        40.08        16.14         0.79 

$`10P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 
        6.97         4.64         7.43        30.90         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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73        12.43         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       20.55         8.05         0.56        12.95         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        19.50        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        19.17        14.79         0.26        15.85         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        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51         8.98         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        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        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        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         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        21.99         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       15.02        28.96        79.07        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
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-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        12.33        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-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
        9.76         2.96        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62        16.24        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        5.03        13.58        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       14.27        12.59        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.81        27.42        21.21         3.45         3.39         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        5.19        13.08        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI 
       37.64         3.72        19.73         9.86        18.21        61.25 
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        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       27.35        64.57        14.33        65.16        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        52.24         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U 
        6.58        64.18        21.04         2.66        42.54        22.09 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        32.94        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       21.11        12.43        10.62 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.00 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            115.69             122.30 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             14.17              12.79 
[1] "0.1 - 115.7 (14.2)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.4"
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       2       12       38       27        37        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           0         14          9          6        8
  10P LOSS WILD-TYPE         4         71         53         35       38
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  2                 12
  STAGE IB                  3                 38
  STAGE II                  4                 27
  STAGE IIA                 1                 37
  STAGE IIB                12                 43
  STAGE III                 0                  4
  STAGE IIIA               14                 71
  STAGE IIIB                9                 53
  STAGE IIIC                6                 35
  STAGE IV                  8                 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
  10P LOSS MUTATED     4  15  30  11
  10P LOSS WILD-TYPE  18  75 165 108
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                4                 18
  T2               15                 75
  T3               30                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    10  18  16  17
  10P LOSS WILD-TYPE 119 100  68  72
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               10                119
  N1               18                100
  N2               16                 68
  N3               17                 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"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    57   3
  10P LOSS WILD-TYPE 330  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     57    3
  10P LOSS WILD-TYPE  330   27
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               57                330
  1                3                 27
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    20  44
  10P LOSS WILD-TYPE 138 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     20   44
  10P LOSS WILD-TYPE  138  234
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               20                138
  MALE                 44                234
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10P LOSS MUTATED                                       6
  10P LOSS WILD-TYPE                                    65
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                       20
  10P LOSS WILD-TYPE                                                    142
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                                  12
  10P LOSS WILD-TYPE                                                                69
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  10P LOSS MUTATED                                                 14
  10P LOSS WILD-TYPE                                               64
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10P LOSS MUTATED                                                          6
  10P LOSS WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  10P LOSS MUTATED                                                           2
  10P LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10P LOSS MUTATED                                          3
  10P LOSS WILD-TYPE                                       10
D60V8, multiclass
                                                                   clus
vv                                                                  10P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  10P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           142
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  64
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          10
[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"
D60V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  63
  10P LOSS WILD-TYPE   5 367
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   63
  10P LOSS WILD-TYPE    5  367
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 1                  5
  YES               63                367
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    51   3   1   5
  10P LOSS WILD-TYPE 296  15  18  20
D60V10, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               51                296
  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       9                         3
  10P LOSS WILD-TYPE    79                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           0    43
  10P LOSS WILD-TYPE                                         1   231
D60V12, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                                    9                 79
  BLACK OR AFRICAN AMERICAN                                3                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   43                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"
D60V13, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  43
  10P LOSS WILD-TYPE   3 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   43
  10P LOSS WILD-TYPE    3  270
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               43                270
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    38  25
  10Q LOSS WILD-TYPE 216 125
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                63                341 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                25                125 
$`10Q LOSS MUTATED`
TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8291 
       19.56        18.35        19.33         3.45        11.44        16.31 
TCGA-BR-8365 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A4CQ 
       17.52         5.39         9.21        20.22         9.86        22.26 
TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-4440 
        3.25         0.07         0.10        12.43         7.99         4.01 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6521 
       12.03        18.97        22.98         4.01        19.13        18.54 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-EQ-8122 TCGA-FP-7829 
       10.26        15.22        15.98        12.79         7.99        19.53 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 
        0.56         5.52         0.23         5.92        14.17        12.10 
TCGA-HU-A4GH TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RP 
       11.77        27.42        18.81        18.38         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-RD-A8N6 
        6.74         6.51        37.64        45.67         8.52         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PE 
        5.79        48.79         5.46        13.02        18.48        22.19 
TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A94O TCGA-VQ-A94T 
       17.85        36.69        18.74         9.50        21.04        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       40.08        32.94         0.79 

$`10Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        6.97         4.64         7.43        30.90         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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       13.08         0.26        22.19         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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       15.85         3.72        25.18         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44        15.68         8.22        10.68        12.56 
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        13.41        13.51 
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        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        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        13.64        11.57         5.13         2.83        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         3.42         9.34        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         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       47.05        19.07        21.99         0.00         9.01         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-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       12.66        11.93        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       13.35        17.19        10.55        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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        2.96        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62        16.24        14.47        72.23        21.27        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-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       13.58        18.08        26.47         1.51        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        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         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
        9.67         8.88         8.81        21.21         3.45         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        5.36         5.19        13.08        12.59         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73         9.86        18.21        61.25         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 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       26.24        27.35        64.57        14.33        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.93        61.22        20.81        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        7.36         9.73        52.24         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58         5.72        64.18         2.66        42.54 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       22.09        18.41        28.41        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        21.11        12.43        10.62 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             48.79             122.30 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             12.43              12.89 
[1] "0.1 - 48.8 (12.4)"  "0.0 - 122.3 (12.9)"
[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        3         3        10
  10Q LOSS WILD-TYPE       2       11       38       28        35        45
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           0         16          7         10        7
  10Q LOSS WILD-TYPE         4         69         55         31       39
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  3                 11
  STAGE IB                  3                 38
  STAGE II                  3                 28
  STAGE IIA                 3                 35
  STAGE IIB                10                 45
  STAGE III                 0                  4
  STAGE IIIA               16                 69
  STAGE IIIB                7                 55
  STAGE IIIC               10                 31
  STAGE IV                  7                 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
  10Q LOSS MUTATED     5  14  29  15
  10Q LOSS WILD-TYPE  17  76 166 104
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                5                 17
  T2               14                 76
  T3               29                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    11  18  15  20
  10Q LOSS WILD-TYPE 118 100  69  69
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               11                118
  N1               18                100
  N2               15                 69
  N3               20                 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"
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    57   6
  10Q LOSS WILD-TYPE 330  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     57    6
  10Q LOSS WILD-TYPE  330   24
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               57                330
  1                6                 24
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    23  44
  10Q LOSS WILD-TYPE 135 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     23   44
  10Q LOSS WILD-TYPE  135  234
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               23                135
  MALE                 44                234
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10Q LOSS MUTATED                                       5
  10Q LOSS WILD-TYPE                                    66
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                       20
  10Q LOSS WILD-TYPE                                                    142
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                                  15
  10Q LOSS WILD-TYPE                                                                66
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  10Q LOSS MUTATED                                                 17
  10Q LOSS WILD-TYPE                                               61
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10Q LOSS MUTATED                                                          5
  10Q LOSS WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  10Q LOSS MUTATED                                                           1
  10Q LOSS WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10Q LOSS MUTATED                                          3
  10Q LOSS WILD-TYPE                                       10
D61V8, multiclass
                                                                   clus
vv                                                                  10Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  10Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           142
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          10
[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"
D61V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  66
  10Q LOSS WILD-TYPE   5 364
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   66
  10Q LOSS WILD-TYPE    5  364
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 1                  5
  YES               66                364
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    52   2   3   4
  10Q LOSS WILD-TYPE 295  16  16  21
D61V10, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               52                295
  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                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           0    42
  10Q LOSS WILD-TYPE                                         1   232
D61V12, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                                   12                 76
  BLACK OR AFRICAN AMERICAN                                4                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   42                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"
D61V13, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  46
  10Q LOSS WILD-TYPE   3 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   46
  10Q LOSS WILD-TYPE    3  267
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               46                267
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    34  27
  11P LOSS WILD-TYPE 220 123
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                61                343 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                27                123 
$`11P LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4279 TCGA-BR-6564 TCGA-BR-7723 TCGA-BR-8080 
        6.61         6.97         9.57        26.10        28.73         9.60 
TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CD-5800 
        2.66         7.40         1.48         0.72         3.25        13.15 
TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4443 TCGA-CG-4444 
        0.30         0.07         3.42        12.43        29.98        47.05 
TCGA-CG-4460 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-5579 
       21.99        30.97        12.03         4.01        12.66        11.93 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8578 
       20.55        18.54        10.26        15.22        15.98        21.14 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-A72C TCGA-FP-8211 TCGA-HJ-7597 TCGA-HU-8245 
        7.40         0.62        11.38        13.58        26.47        12.59 
TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
       14.17        22.75         2.10        23.84        12.30         9.67 
TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-R5-A7O7 TCGA-R5-A7ZE 
        3.39         5.19         6.44         6.74        45.67        18.21 
TCGA-RD-A8MW TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PS 
       37.91        48.79        13.25        34.45        17.85        13.35 
TCGA-VQ-A8PU TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
       27.35        52.24         9.04         4.54        21.04        42.54 
TCGA-VQ-AA6K 
       12.43 

$`11P LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 
        4.64         7.43        18.35        30.90         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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
       12.26        20.55         8.05         0.56        12.95        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         6.18        19.50        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        19.17        14.79         0.26        15.85 
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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
       22.26        13.41        13.51        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        12.82         0.66        19.36        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        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        2.83        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         9.34        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         0.10        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-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-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        22.98         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-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        69.04        21.07         7.99        12.36 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       19.13        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        14.66        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        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        8.38         4.34         7.13         7.99        16.24        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-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       17.06        59.54         5.03         0.56         5.52         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       18.08         1.51         5.92        14.27        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
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         6.25        10.19         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.95        19.36         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO 
        3.45        18.81        18.38         5.36        13.08         1.41 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51         5.56         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
        2.53         5.56        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       19.73         9.86         8.52        61.25         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        35.24        21.73        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        28.96        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        26.24        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
        1.71        36.16         7.36         9.50         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T 
       55.43         6.58         5.72        64.18         2.66        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       22.09        18.41        40.08        28.41        32.94        29.98 
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        21.11        10.62 
TCGA-ZQ-A9CR 
        0.79 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.00 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             52.24             122.30 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             12.59              12.89 
[1] "0.1 - 52.2 (12.6)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.2"
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       3       13       35       25        34        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           0         18          5          7        9
  11P LOSS WILD-TYPE         4         67         57         34       37
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  1                 13
  STAGE IB                  6                 35
  STAGE II                  6                 25
  STAGE IIA                 4                 34
  STAGE IIB                 5                 50
  STAGE III                 0                  4
  STAGE IIIA               18                 67
  STAGE IIIB                5                 57
  STAGE IIIC                7                 34
  STAGE IV                  9                 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 LOSS MUTATED     2  19  28  13
  11P LOSS WILD-TYPE  20  71 167 106
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                2                 20
  T2               19                 71
  T3               28                167
  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
  11P LOSS MUTATED    13  20  15  13
  11P LOSS WILD-TYPE 116  98  69  76
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               13                116
  N1               20                 98
  N2               15                 69
  N3               13                 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"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    52   7
  11P LOSS WILD-TYPE 335  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     52    7
  11P LOSS WILD-TYPE  335   23
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               52                335
  1                7                 23
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    19  43
  11P LOSS WILD-TYPE 139 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     19   43
  11P LOSS WILD-TYPE  139  235
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               19                139
  MALE                 43                235
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11P LOSS MUTATED                                       7
  11P LOSS WILD-TYPE                                    64
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                       16
  11P LOSS WILD-TYPE                                                    146
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                                  15
  11P LOSS WILD-TYPE                                                                66
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  11P LOSS MUTATED                                                 16
  11P LOSS WILD-TYPE                                               62
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11P LOSS MUTATED                                                          2
  11P LOSS WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  11P LOSS MUTATED                                                           4
  11P LOSS WILD-TYPE                                                         4
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11P LOSS MUTATED                                          2
  11P LOSS WILD-TYPE                                       11
D62V8, multiclass
                                                                   clus
vv                                                                  11P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  11P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  62
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          11
[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"
D62V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  62
  11P LOSS WILD-TYPE   6 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   62
  11P LOSS WILD-TYPE    6  368
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 0                  6
  YES               62                368
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    44   3   5   4
  11P LOSS WILD-TYPE 303  15  14  21
D62V10, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               44                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                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           0    38
  11P LOSS WILD-TYPE                                         1   236
D62V12, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                1                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   38                236
[1] 4 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   3 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1   43
  11P LOSS WILD-TYPE    3  270
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               43                270
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    31  28
  11Q LOSS WILD-TYPE 223 122
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                59                345 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                28                122 
$`11Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4279 TCGA-BR-6709 TCGA-BR-7723 TCGA-BR-8080 
        6.61         6.97         9.57        12.16        28.73         9.60 
TCGA-BR-8289 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        2.66        17.52        20.22        22.26         1.48         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8527 
       13.51         1.15         3.25        13.15         0.30         0.07 
TCGA-CD-A48A TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-5724 TCGA-D7-5578 
       12.43         8.05        29.98        12.03        12.03        12.66 
TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-A74A TCGA-EQ-5647 
       11.93        18.54        10.26        15.98         7.40         0.62 
TCGA-FP-7916 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8610 
       14.07        13.58         0.23        26.47        14.17         0.76 
TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-A6RL TCGA-IN-A6RP 
       22.75         2.10        23.84         9.67         5.19         6.44 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A805 TCGA-RD-A8MW TCGA-VQ-A8DT TCGA-VQ-A8DV 
       45.67        18.21         9.24        37.91        48.79        13.25 
TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91Q TCGA-VQ-A91Z 
       34.45        17.85        13.35        27.35        20.81        52.24 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6K 
        9.04        21.04        42.54        11.24        12.43 

$`11Q LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 
        4.64         7.43        18.35        30.90         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-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-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
       12.26        20.55         8.05         0.56        12.95        16.31 
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        19.50        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        19.17        14.79         0.26        15.85 
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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
       10.68        12.56        13.87         7.53         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         8.98        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
        0.66        19.36         0.46        20.65        20.42        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 
       11.57         5.13         2.83        13.18         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.13         0.13         0.10         3.42         9.34 
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         0.10        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-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
       54.08         4.01        14.01        47.05        19.07        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
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-5727 TCGA-CG-5728 
        0.99       105.07        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 
        4.01        69.04        21.07         7.99        12.36        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-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        12.79        10.55        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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
        2.96        15.65         8.38         4.34         7.13         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        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-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        5.52        18.08         1.51         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        12.10        10.62        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        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         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26        12.95        19.36        12.30         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       27.42        21.21         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        5.36        13.08         1.41         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        5.56         1.81         7.82        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
       60.56        20.15        37.64         3.72        19.73         9.86 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        61.25         6.08         4.60        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67       122.30        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-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92         5.46        13.02        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        27.88        32.48         7.73        28.96        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-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        26.24        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       64.18         2.66        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       32.94        29.98        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        10.62         0.79 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.07               0.00 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             52.24             122.30 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             12.43              12.89 
[1] "0.1 - 52.2 (12.4)"  "0.0 - 122.3 (12.9)"
[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         2         4
  11Q LOSS WILD-TYPE       3       11       39       23        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           0         15          9          8        8
  11Q LOSS WILD-TYPE         4         70         53         33       38
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  3                 11
  STAGE IB                  2                 39
  STAGE II                  8                 23
  STAGE IIA                 2                 36
  STAGE IIB                 4                 51
  STAGE III                 0                  4
  STAGE IIIA               15                 70
  STAGE IIIB                9                 53
  STAGE IIIC                8                 33
  STAGE IV                  8                 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
  11Q LOSS MUTATED     4  13  28  15
  11Q LOSS WILD-TYPE  18  77 167 104
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                4                 18
  T2               13                 77
  T3               28                167
  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 120  99  70  72
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                9                120
  N1               19                 99
  N2               14                 70
  N3               17                 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"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    50   5
  11Q LOSS WILD-TYPE 337  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     50    5
  11Q LOSS WILD-TYPE  337   25
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               50                337
  1                5                 25
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    17  43
  11Q LOSS WILD-TYPE 141 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     17   43
  11Q LOSS WILD-TYPE  141  235
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               17                141
  MALE                 43                235
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11Q LOSS MUTATED                                       5
  11Q LOSS WILD-TYPE                                    66
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                       18
  11Q LOSS WILD-TYPE                                                    144
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                                  13
  11Q LOSS WILD-TYPE                                                                68
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  11Q LOSS MUTATED                                                 16
  11Q LOSS WILD-TYPE                                               62
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11Q LOSS MUTATED                                                          3
  11Q LOSS WILD-TYPE                                                       18
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  11Q LOSS MUTATED                                                           2
  11Q LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11Q LOSS MUTATED                                          3
  11Q LOSS WILD-TYPE                                       10
D63V8, multiclass
                                                                   clus
vv                                                                  11Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  11Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           144
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  62
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          10
[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"
D63V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0  60
  11Q LOSS WILD-TYPE   6 370
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   60
  11Q LOSS WILD-TYPE    6  370
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 0                  6
  YES               60                370
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    43   4   2   4
  11Q LOSS WILD-TYPE 304  14  17  21
D63V10, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               43                304
  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                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           0    38
  11Q LOSS WILD-TYPE                                         1   236
D63V12, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                                   13                 75
  BLACK OR AFRICAN AMERICAN                                1                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   38                236
[1] 4 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  42
  11Q LOSS WILD-TYPE   3 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   42
  11Q LOSS WILD-TYPE    3  271
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               42                271
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    28  28
  12P LOSS WILD-TYPE 226 122
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                56                348 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                28                122 
$`12P LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7901 
        6.61         6.18        17.29        35.24        15.42         3.45 
TCGA-BR-8060 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4J6 
       11.44         5.39         9.21         9.86         8.22         0.66 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 
       13.15         0.30         0.07         0.13         3.42        11.31 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4477 TCGA-CG-5725 
       12.20        20.02         7.99        29.98        30.97        15.02 
TCGA-CG-5732 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A4YT TCGA-EQ-5647 TCGA-EQ-8122 
       69.04        15.22        12.33        14.27         0.62         7.99 
TCGA-F1-6875 TCGA-FP-8631 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-HU-A4H4 
       72.23         0.56        12.59        11.77        12.95        23.84 
TCGA-HU-A4H5 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-R5-A7O7 TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       12.30         5.19        13.08        45.67         5.46        13.02 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91X 
       12.79         2.70        13.35        27.35        14.33         9.50 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 
       52.24         2.01         4.54        21.04        11.24        40.08 
TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       16.14         0.79 

$`12P LOSS WILD-TYPE`
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-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 
        6.97         4.64         7.43        18.35        30.90         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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       32.94        12.82         9.21        24.76        23.93        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73        12.43         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
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        19.50        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       15.85         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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       11.54        15.81        16.44        15.68        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        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 
       12.82        19.36        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        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       13.18         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        12.43        11.61         6.58         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.98        12.79        10.55        11.31 
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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        2.96        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        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-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        5.52         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       14.27        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10        19.36 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RP 
       18.81         3.39        18.38         5.36         1.41         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         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
       13.51         2.53         5.56        60.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73         9.86        18.21         8.52        61.25 
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-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.25        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK 
       34.29        46.26        16.31        22.19         2.50        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        26.24        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y 
       20.81        22.68         1.71        36.16         7.36         9.73 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        9.04        55.43         6.58         5.72        64.18         2.66 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.54        22.09        18.41        28.41        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        54.12        26.04        21.11        12.43        10.62 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.07               0.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             72.23             122.30 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             12.25              13.13 
[1] "0.1 - 72.2 (12.2)"  "0.0 - 122.3 (13.1)"
[1] "hr=" "1.6"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         0        3        8        4         6         5
  12P LOSS WILD-TYPE       3       11       33       27        32        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           0         13          8          7        5
  12P LOSS WILD-TYPE         4         72         54         34       41
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  3                 11
  STAGE IB                  8                 33
  STAGE II                  4                 27
  STAGE IIA                 6                 32
  STAGE IIB                 5                 50
  STAGE III                 0                  4
  STAGE IIIA               13                 72
  STAGE IIIB                8                 54
  STAGE IIIC                7                 34
  STAGE IV                  5                 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
  12P LOSS MUTATED     3  15  30  11
  12P LOSS WILD-TYPE  19  75 165 108
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                3                 19
  T2               15                 75
  T3               30                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
  12P LOSS MUTATED    20  13  13  13
  12P LOSS WILD-TYPE 109 105  71  76
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               20                109
  N1               13                105
  N2               13                 71
  N3               13                 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 334  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     53    4
  12P LOSS WILD-TYPE  334   26
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               53                334
  1                4                 26
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    25  36
  12P LOSS WILD-TYPE 133 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     25   36
  12P LOSS WILD-TYPE  133  242
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               25                133
  MALE                 36                242
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12P LOSS MUTATED                                       3
  12P LOSS WILD-TYPE                                    68
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                       23
  12P LOSS WILD-TYPE                                                    139
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                                  13
  12P LOSS WILD-TYPE                                                                68
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  12P LOSS MUTATED                                                 18
  12P LOSS WILD-TYPE                                               60
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12P LOSS MUTATED                                                          0
  12P LOSS WILD-TYPE                                                       21
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  12P LOSS MUTATED                                                           3
  12P LOSS WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12P LOSS MUTATED                                          1
  12P LOSS WILD-TYPE                                       12
D64V8, multiclass
                                                                   clus
vv                                                                  12P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  12P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  60
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          12
[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"
D64V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  60
  12P LOSS WILD-TYPE   5 370
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   60
  12P LOSS WILD-TYPE    5  370
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 1                  5
  YES               60                370
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    44   2   4   5
  12P LOSS WILD-TYPE 303  16  15  20
D64V10, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               44                303
  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                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           0    35
  12P LOSS WILD-TYPE                                         1   239
D64V12, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                                   13                 75
  BLACK OR AFRICAN AMERICAN                                3                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   35                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"
D64V13, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  37
  12P LOSS WILD-TYPE   3 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   37
  12P LOSS WILD-TYPE    3  276
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               37                276
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    22  25
  12Q LOSS WILD-TYPE 232 125
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                47                357 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                25                125 
$`12Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8060 
        6.61        17.29        35.24        15.42         3.45        11.44 
TCGA-BR-8286 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4J6 
       12.95         5.39         9.21         9.86         8.22         0.66 
TCGA-CD-5802 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
        0.30         3.42        11.31        12.20        20.02         7.99 
TCGA-CG-4443 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6528 TCGA-D7-A6F2 TCGA-EQ-5647 
       29.98        15.02        69.04        15.22        15.65         0.62 
TCGA-EQ-8122 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-IN-A6RP 
        7.99        13.58         0.56        11.77        12.95         6.44 
TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PH 
       37.64        45.67        18.21         5.46        18.48        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94O 
       17.85        13.35        27.35        52.24         4.54        21.04 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       11.24        40.08        16.14        12.43         0.79 

$`12Q LOSS WILD-TYPE`
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-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       28.01        18.15        15.32        28.73        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05         0.56         2.66        16.31 
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        19.50        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       15.85         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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       11.54        15.81        16.44        15.68        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        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 
       12.82        19.36        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        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.13         0.10         9.34        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        1.02         8.05        54.08         4.01        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        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 
       12.36        12.66        11.93        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-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO 
        2.96         8.38         4.34         7.40         7.13        16.24 
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-A4BF 
       14.07        22.29        17.06        59.54         5.03         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.23        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        12.30         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        5.19        13.08         1.41         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        5.56         1.81         7.82        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF 
       60.56        20.15         3.72        19.73         9.86         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         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 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        16.31        22.19         2.50 
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        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        7.36         9.50         9.73         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U 
        6.58         5.72        64.18         2.66        42.54        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        28.41        32.94        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        21.11        10.62 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               0.3                0.0 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             69.04             122.30 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             12.79              12.82 
[1] "0.3 - 69.0 (12.8)"  "0.0 - 122.3 (12.8)"
[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       3       12       36       28        32        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0         10          7          8        3
  12Q LOSS WILD-TYPE         4         75         55         33       43
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  2                 12
  STAGE IB                  5                 36
  STAGE II                  3                 28
  STAGE IIA                 6                 32
  STAGE IIB                 6                 49
  STAGE III                 0                  4
  STAGE IIIA               10                 75
  STAGE IIIB                7                 55
  STAGE IIIC                8                 33
  STAGE IV                  3                 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
  12Q LOSS MUTATED     3   7  30  10
  12Q LOSS WILD-TYPE  19  83 165 109
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                3                 19
  T2                7                 83
  T3               30                165
  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    16  10  11  13
  12Q LOSS WILD-TYPE 113 108  73  76
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               16                113
  N1               10                108
  N2               11                 73
  N3               13                 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"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    45   2
  12Q LOSS WILD-TYPE 342  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     45    2
  12Q LOSS WILD-TYPE  342   28
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               45                342
  1                2                 28
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    20  32
  12Q LOSS WILD-TYPE 138 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     20   32
  12Q LOSS WILD-TYPE  138  246
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               20                138
  MALE                 32                246
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12Q LOSS MUTATED                                       3
  12Q LOSS WILD-TYPE                                    68
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                       21
  12Q LOSS WILD-TYPE                                                    141
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                                  12
  12Q LOSS WILD-TYPE                                                                69
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  12Q LOSS MUTATED                                                 15
  12Q LOSS WILD-TYPE                                               63
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12Q LOSS MUTATED                                                          0
  12Q LOSS WILD-TYPE                                                       21
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  12Q LOSS MUTATED                                                           0
  12Q LOSS WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12Q LOSS MUTATED                                          1
  12Q LOSS WILD-TYPE                                       12
D65V8, multiclass
                                                                   clus
vv                                                                  12Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  12Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  63
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          12
[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"
D65V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  51
  12Q LOSS WILD-TYPE   5 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   51
  12Q LOSS WILD-TYPE    5  379
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 1                  5
  YES               51                379
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    36   4   2   3
  12Q LOSS WILD-TYPE 311  14  17  22
D65V10, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               36                311
  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       8                         2
  12Q LOSS WILD-TYPE    80                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0    34
  12Q LOSS WILD-TYPE                                         1   240
D65V12, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                                    8                 80
  BLACK OR AFRICAN AMERICAN                                2                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   34                240
[1] 4 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   3 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   30
  12Q LOSS WILD-TYPE    3  283
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               30                283
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    17  14
  13Q LOSS WILD-TYPE 237 136
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                31                373 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                136 
$`13Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7716 
        6.61         6.97        17.29        26.10        12.16        28.01 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A4IY TCGA-CD-8526 
        7.40        19.50        20.22         9.86        12.89         0.07 
TCGA-CD-8533 TCGA-CG-4301 TCGA-CG-4466 TCGA-CG-4475 TCGA-D7-6525 TCGA-D7-8575 
        0.13         3.02        18.97        22.98        13.35        18.21 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-FP-7916 TCGA-FP-8211 TCGA-HU-A4GC TCGA-HU-A4H2 
       21.14        16.44        14.07        13.58         3.25        12.95 
TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-RD-A7BS TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A91Z 
        5.36         6.74        11.05         7.73         1.87        52.24 
TCGA-VQ-A925 
        4.54 

$`13Q LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
        9.21        24.76        35.24        23.93        15.42        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       18.71        17.49        14.43        11.44         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
       16.31         2.20        15.58         6.18        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        19.17        14.79         0.26        15.85 
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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81        16.44        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         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 
       12.82         0.66        19.36        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        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        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         0.10        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-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         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-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        17.19        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        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       19.50        17.19        14.66        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        7.40         7.13         0.62         7.99        16.24        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-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       17.06        59.54         5.03         0.56         5.52         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20        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-A4H3 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.30         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        1.41         6.44        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT 
        8.52        61.25         6.08         4.60         9.24         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        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
       32.48        28.96        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70        17.85         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
       64.18        21.04         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        40.08        28.41        32.94        29.98        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        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.00 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             52.24             122.30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             12.89              12.82 
[1] "0.1 - 52.2 (12.9)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.5"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         0        1        4        1         1         5
  13Q LOSS WILD-TYPE       3       13       37       30        37        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           0         11          5          3        3
  13Q LOSS WILD-TYPE         4         74         57         38       43
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  1                 13
  STAGE IB                  4                 37
  STAGE II                  1                 30
  STAGE IIA                 1                 37
  STAGE IIB                 5                 50
  STAGE III                 0                  4
  STAGE IIIA               11                 74
  STAGE IIIB                5                 57
  STAGE IIIC                3                 38
  STAGE IV                  3                 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
  13Q LOSS MUTATED     2   6  19   8
  13Q LOSS WILD-TYPE  20  84 176 111
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                2                 20
  T2                6                 84
  T3               19                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     8  12   7   7
  13Q LOSS WILD-TYPE 121 106  77  82
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                8                121
  N1               12                106
  N2                7                 77
  N3                7                 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"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    30   1
  13Q LOSS WILD-TYPE 357  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     30    1
  13Q LOSS WILD-TYPE  357   29
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               30                357
  1                1                 29
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    15  20
  13Q LOSS WILD-TYPE 143 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     15   20
  13Q LOSS WILD-TYPE  143  258
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               15                143
  MALE                 20                258
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  13Q LOSS MUTATED                                       6
  13Q LOSS WILD-TYPE                                    65
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                       16
  13Q LOSS WILD-TYPE                                                    146
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                                   3
  13Q LOSS WILD-TYPE                                                                78
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  13Q LOSS MUTATED                                                  7
  13Q LOSS WILD-TYPE                                               71
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  13Q LOSS MUTATED                                                          1
  13Q LOSS WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  13Q LOSS MUTATED                                                           0
  13Q LOSS WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  13Q LOSS MUTATED                                          1
  13Q LOSS WILD-TYPE                                       12
D66V8, multiclass
                                                                   clus
vv                                                                  13Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  13Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 78
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  71
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          12
[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"
D66V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     2  33
  13Q LOSS WILD-TYPE   4 397
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   33
  13Q LOSS WILD-TYPE    4  397
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 2                  4
  YES               33                397
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    25   3   2   4
  13Q LOSS WILD-TYPE 322  15  17  21
D66V10, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               25                322
  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       7                         0
  13Q LOSS WILD-TYPE    81                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           0    23
  13Q LOSS WILD-TYPE                                         1   251
D66V12, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                                    7                 81
  BLACK OR AFRICAN AMERICAN                                0                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   23                251
[1] 4 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     0  26
  13Q LOSS WILD-TYPE   4 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0   26
  13Q LOSS WILD-TYPE    4  287
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               26                287
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    66  37
  14Q LOSS WILD-TYPE 188 113
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               103                301 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                37                113 
$`14Q LOSS MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4279 TCGA-BR-6458 
       19.56        11.01         9.44         6.61         9.57        19.33 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 
       26.10         9.17        12.16        31.20        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8286 TCGA-BR-8289 
       28.01        28.73        18.71        17.49        12.95         2.66 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 
       14.79         0.26         5.39        25.18         9.21        11.54 
TCGA-BR-8686 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       15.68         1.48         0.72         0.66        19.36         0.46 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 
       20.65         1.15        13.18         0.07         0.07         0.07 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
        0.13         0.13        11.31        12.20        20.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4477 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        8.05        54.08        30.97        20.55        18.84        18.54 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX 
       17.19        10.26        15.98        14.66        16.44        11.31 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 
        2.96         7.40         7.99        11.38        14.07        17.06 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GH 
        0.56        26.47        12.59        14.17         3.25        11.77 
TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RL 
        8.98         2.10        23.84        27.42        21.21         5.19 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A93H TCGA-RD-A7C1 
        6.44         6.74         1.81         2.53        37.64        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 
       35.24         7.73        46.26        12.79         2.70        17.85 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91Z 
       27.35        64.57        14.33        65.16        20.81        52.24 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G 
       64.18        21.04        22.09        32.94        29.98        26.04 
TCGA-ZQ-A9CR 
        0.79 

$`14Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 
       13.87        17.29        13.68        39.12        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       18.05        19.89         8.98        21.11        30.90        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       12.82         9.21        24.76        23.93        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 
       12.43         3.45         9.07        12.76        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
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-8382 
        4.31        14.04         3.32        11.80        19.17        15.85 
TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        22.26        13.41        13.51        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI 
       14.17         0.53        12.82        13.51        20.42        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       11.57         5.13         2.83         3.25        13.15         0.30 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         0.10         3.42         9.34        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        1.02         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 
       12.36        12.66        11.93        19.13        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       13.35        15.22        12.79        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       13.71        11.24        11.44         9.76        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         0.62        16.24        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-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       13.58         5.52         0.23        18.08         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20        22.75        25.81 
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         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26        12.95        19.36        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.81         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
       13.08         1.41        12.59         6.51         5.56         7.82 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         5.56        60.56        20.15         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        9.86        45.67        18.21         8.52        61.25         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-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 
       19.04         5.79         0.92        48.79        13.25        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       34.45        27.88        32.48        28.96        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       22.19         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       13.35        26.24        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        5.72         2.66        42.54        11.24        18.41        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       28.41        17.13        54.12        16.14        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.00 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            115.69             122.30 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             14.07              12.76 
[1] "0.1 - 115.7 (14.1)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         0        2        8       11        12        14
  14Q LOSS WILD-TYPE       3       12       33       20        26        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           0         27         17         10        5
  14Q LOSS WILD-TYPE         4         58         45         31       41
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  2                 12
  STAGE IB                  8                 33
  STAGE II                 11                 20
  STAGE IIA                12                 26
  STAGE IIB                14                 41
  STAGE III                 0                  4
  STAGE IIIA               27                 58
  STAGE IIIB               17                 45
  STAGE IIIC               10                 31
  STAGE IV                  5                 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
  14Q LOSS MUTATED     3  20  56  27
  14Q LOSS WILD-TYPE  19  70 139  92
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                3                 19
  T2               20                 70
  T3               56                139
  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 98 91 57 70
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               31                 98
  N1               27                 91
  N2               27                 57
  N3               19                 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"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    99   3
  14Q LOSS WILD-TYPE 288  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     99    3
  14Q LOSS WILD-TYPE  288   27
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               99                288
  1                3                 27
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    38  72
  14Q LOSS WILD-TYPE 120 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     38   72
  14Q LOSS WILD-TYPE  120  206
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               38                120
  MALE                 72                206
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  14Q LOSS MUTATED                                      14
  14Q LOSS WILD-TYPE                                    57
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                       40
  14Q LOSS WILD-TYPE                                                    122
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                                  25
  14Q LOSS WILD-TYPE                                                                56
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  14Q LOSS MUTATED                                                 22
  14Q LOSS WILD-TYPE                                               56
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  14Q LOSS MUTATED                                                          2
  14Q LOSS WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  14Q LOSS MUTATED                                                           2
  14Q LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  14Q LOSS MUTATED                                          5
  14Q LOSS WILD-TYPE                                        8
D67V8, multiclass
                                                                   clus
vv                                                                  14Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                22
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         5
                                                                   clus
vv                                                                  14Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  56
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[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"
D67V9, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1 109
  14Q LOSS WILD-TYPE   5 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1  109
  14Q LOSS WILD-TYPE    5  321
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 1                  5
  YES              109                321
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    90   3   2   7
  14Q LOSS WILD-TYPE 257  15  17  18
D67V10, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               90                257
  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                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           0    74
  14Q LOSS WILD-TYPE                                         1   200
D67V12, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                                   24                 64
  BLACK OR AFRICAN AMERICAN                                3                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   74                200
[1] 4 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  82
  14Q LOSS WILD-TYPE   4 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   82
  14Q LOSS WILD-TYPE    4  231
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               82                231
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    55  27
  15Q LOSS WILD-TYPE 199 123
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                82                322 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                27                123 
$`15Q LOSS MUTATED`
TCGA-B7-A5TJ TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8289 
       11.01        35.24        28.73         3.45        12.95         2.66 
TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4J1 TCGA-BR-A4PD 
       14.79         5.39        15.68        10.68         0.72        20.65 
TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8535 
       13.64        13.18         0.07         0.07         0.16         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4440 
       12.43        11.61        12.20        20.02         7.99         4.01 
TCGA-CG-4466 TCGA-CG-5719 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       18.97         1.02        12.03        12.66        19.13        20.55 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4YU 
       17.19        10.26        15.22        12.79        14.66        16.44 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-FP-7998 
       11.31         2.96        15.65         7.40         7.99        22.29 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52         0.23        26.47        12.59        14.17        12.10 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
       22.75         8.98         6.25         2.10        12.95        23.84 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NU 
        9.67        27.42         5.36         5.19         6.44         1.81 
TCGA-IP-7968 TCGA-MX-A663 TCGA-R5-A7ZF TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW 
        2.53         9.86         8.52        11.05        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PS 
      115.69        35.61         5.79        48.79         5.46        13.35 
TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 
       27.35        65.16         1.71         9.50         9.73         9.04 
TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F 
       42.54        40.08        29.98        54.12 

$`15Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       23.93        15.42        28.01        18.15        15.32        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        12.76        18.71        17.49        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
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-8381 
        4.31        14.04         3.32        11.80        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       15.85         3.72        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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        0.49        11.54        15.81        16.44         9.86         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        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 
       12.82         0.66        19.36        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       11.31         6.58         0.10        12.62         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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.36        11.93        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       13.35        15.98        10.55        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-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        11.44         9.76         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62        16.24        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-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       13.58         0.56        18.08         1.51         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        25.81        11.77        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        10.19         0.26        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39        18.38        13.08         1.41         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         5.56         7.82        13.51         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE 
       20.15        37.64         3.72        19.73        45.67        18.21 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW 
       61.25         6.08         4.60         9.24         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
      122.30        40.64       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       16.87        19.04         0.92        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        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-A91A TCGA-VQ-A91D 
       15.65        26.24        64.57        14.33        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V 
       11.93        61.22        18.74        20.81        22.68        36.16 
TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        7.36        52.24         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U 
        5.72        64.18        21.04         2.66        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        28.41        32.94        17.13        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.07               0.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            115.69             122.30 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            12.150             13.115 
[1] "0.1 - 115.7 (12.1)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         0        0        9        7         8         9
  15Q LOSS WILD-TYPE       3       14       32       24        30        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           0         25         13          8        7
  15Q LOSS WILD-TYPE         4         60         49         33       39
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  0                 14
  STAGE IB                  9                 32
  STAGE II                  7                 24
  STAGE IIA                 8                 30
  STAGE IIB                 9                 46
  STAGE III                 0                  4
  STAGE IIIA               25                 60
  STAGE IIIB               13                 49
  STAGE IIIC                8                 33
  STAGE IV                  7                 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 LOSS MUTATED     2  18  50  17
  15Q LOSS WILD-TYPE  20  72 145 102
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                2                 20
  T2               18                 72
  T3               50                145
  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    22  25  19  19
  15Q LOSS WILD-TYPE 107  93  65  70
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               22                107
  N1               25                 93
  N2               19                 65
  N3               19                 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"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    78   5
  15Q LOSS WILD-TYPE 309  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     78    5
  15Q LOSS WILD-TYPE  309   25
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               78                309
  1                5                 25
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    34  55
  15Q LOSS WILD-TYPE 124 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     34   55
  15Q LOSS WILD-TYPE  124  223
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               34                124
  MALE                 55                223
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  15Q LOSS MUTATED                                      12
  15Q LOSS WILD-TYPE                                    59
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                       26
  15Q LOSS WILD-TYPE                                                    136
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                                  21
  15Q LOSS WILD-TYPE                                                                60
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  15Q LOSS MUTATED                                                 23
  15Q LOSS WILD-TYPE                                               55
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  15Q LOSS MUTATED                                                          1
  15Q LOSS WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  15Q LOSS MUTATED                                                           2
  15Q LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  15Q LOSS MUTATED                                          4
  15Q LOSS WILD-TYPE                                        9
D68V8, multiclass
                                                                   clus
vv                                                                  15Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         4
                                                                   clus
vv                                                                  15Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           136
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           9
[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"
D68V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3  86
  15Q LOSS WILD-TYPE   3 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3   86
  15Q LOSS WILD-TYPE    3  344
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 3                  3
  YES               86                344
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    73   4   3   3
  15Q LOSS WILD-TYPE 274  14  16  22
D68V10, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               73                274
  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                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           0    55
  15Q LOSS WILD-TYPE                                         1   219
D68V12, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                                   23                 65
  BLACK OR AFRICAN AMERICAN                                1                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   55                219
[1] 4 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     1  67
  15Q LOSS WILD-TYPE   3 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   67
  15Q LOSS WILD-TYPE    3  246
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               67                246
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    61  30
  16P LOSS WILD-TYPE 193 120
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                91                313 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                30                120 
$`16P LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 
        6.61         9.21        35.24        15.42        28.01         3.45 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       18.71        11.44         0.69        12.95         2.66        16.31 
TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4CQ 
       17.52        14.79         0.49        11.54         8.22        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5803 TCGA-CD-8524 
        1.48         0.72         1.15        13.64         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
        0.07         0.07         0.16         3.42        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-5724 
       12.20         7.99        29.98        19.07        12.03        12.03 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A6EX TCGA-D7-A6F0 
       11.93        20.55        15.22        12.33        11.31         2.96 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-HU-8243 
       15.65         7.40         7.99        16.24        72.23         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.59        12.10         0.76        22.75        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RN 
        6.25        23.84        12.30         9.67        27.42        13.08 
TCGA-IN-A6RR TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS 
        6.74         5.56        37.64         6.08         9.24        11.05 
TCGA-RD-A7C1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 
       16.67        35.61         5.79        48.79         5.46        18.48 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       46.26        22.19        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       27.35        64.57        36.69         9.50        52.24         9.04 
TCGA-VQ-A92D TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6J 
       64.18        22.09        40.08        32.94        17.13        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`16P LOSS WILD-TYPE`
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-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73        12.43         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.56         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       13.08         0.26        22.19         0.95        26.33         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        19.17         0.26        15.85 
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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44         9.86        15.68        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       13.87         7.53         6.08        13.41        13.51        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        12.82         0.66        19.36 
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        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8527 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.10         0.13         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         9.34        11.31         6.58         0.10        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-4444 TCGA-CG-4460 TCGA-CG-4462 
       54.08         4.01        14.01        47.05        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       69.04        21.07         7.99        12.36        12.66        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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       10.26        15.98        12.79        10.55        11.31        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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 
       14.76        13.71        11.24        11.44         9.76         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        4.34         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-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
       26.47         1.51        14.27        14.17        11.41        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
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        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26         2.10        12.95        19.36         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        5.19         1.41         6.44        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G 
        1.81         7.82        13.51         2.53        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73         9.86        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
       61.25         4.60         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-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
       16.87        19.04         0.92        13.25        13.02        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       34.29        16.31         2.50         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       13.35        26.24        14.33        65.16        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        7.36         9.73         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-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K 
       28.41        29.98        54.12        26.04        16.14        12.43 
TCGA-ZA-A8F6 
       10.62 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             72.23             122.30 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             12.20              13.15 
[1] "0.1 - 72.2 (12.2)"  "0.0 - 122.3 (13.2)"
[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         9        11
  16P LOSS WILD-TYPE       3        9       32       22        29        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           1         24         13          9        6
  16P LOSS WILD-TYPE         3         61         49         32       40
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  5                  9
  STAGE IB                  9                 32
  STAGE II                  9                 22
  STAGE IIA                 9                 29
  STAGE IIB                11                 44
  STAGE III                 1                  3
  STAGE IIIA               24                 61
  STAGE IIIB               13                 49
  STAGE IIIC                9                 32
  STAGE IV                  6                 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
  16P LOSS MUTATED     5  18  51  23
  16P LOSS WILD-TYPE  17  72 144  96
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                5                 17
  T2               18                 72
  T3               51                144
  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
  16P LOSS MUTATED   30 31 17 18
  16P LOSS WILD-TYPE 99 87 67 71
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               30                 99
  N1               31                 87
  N2               17                 67
  N3               18                 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"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    93   3
  16P LOSS WILD-TYPE 294  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     93    3
  16P LOSS WILD-TYPE  294   27
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               93                294
  1                3                 27
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    37  62
  16P LOSS WILD-TYPE 121 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     37   62
  16P LOSS WILD-TYPE  121  216
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               37                121
  MALE                 62                216
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16P LOSS MUTATED                                       9
  16P LOSS WILD-TYPE                                    62
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                       31
  16P LOSS WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                                  19
  16P LOSS WILD-TYPE                                                                62
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  16P LOSS MUTATED                                                 27
  16P LOSS WILD-TYPE                                               51
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16P LOSS MUTATED                                                          8
  16P LOSS WILD-TYPE                                                       13
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  16P LOSS MUTATED                                                           2
  16P LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16P LOSS MUTATED                                          3
  16P LOSS WILD-TYPE                                       10
D69V8, multiclass
                                                                   clus
vv                                                                  16P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  16P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          10
[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"
D69V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     2  97
  16P LOSS WILD-TYPE   4 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2   97
  16P LOSS WILD-TYPE    4  333
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 2                  4
  YES               97                333
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    79   5   2   5
  16P LOSS WILD-TYPE 268  13  17  20
D69V10, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               79                268
  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                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           0    57
  16P LOSS WILD-TYPE                                         1   217
D69V12, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                                   24                 64
  BLACK OR AFRICAN AMERICAN                                4                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   57                217
[1] 4 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   4 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0   68
  16P LOSS WILD-TYPE    4  245
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               68                245
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    71  35
  16Q LOSS WILD-TYPE 183 115
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               106                298 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                35                115 
$`16Q LOSS MUTATED`
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-7197 TCGA-BR-7704 
        9.44         6.61        17.29        26.10         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 
       15.42        28.01        28.73         3.45        18.71        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8365 
        0.69         9.60        12.95         2.66        16.31        17.52 
TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4J1 
       14.79        25.18         0.49        11.54         8.22         0.72 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
       20.65         1.15        13.64        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A486 TCGA-CD-A48A 
        0.07         0.07         0.07         0.16         3.42        12.43 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
       12.20         7.99        29.98        47.05        19.07        12.03 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 
       22.98        30.97        12.03        11.93        20.55        17.19 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A6EX TCGA-D7-A6F0 
       15.22        12.79        18.21        14.27        11.31         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-HU-8243 TCGA-HU-8245 
       15.65         8.38        16.24        72.23         5.92        12.59 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY 
       12.10         0.76        11.77         8.98         6.25         0.26 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN 
       23.84        12.30         9.67        27.42        18.38        13.08 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-R5-A7ZR TCGA-R5-A805 
        5.56        60.56        20.15        37.64         6.08         9.24 
TCGA-RD-A7BS TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 
       11.05        35.61         5.79        48.79         5.46        18.48 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        7.73        46.26        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91S TCGA-VQ-A91X 
        1.87        27.35        64.57        36.69        22.68         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94U 
        9.73        52.24         9.04         4.54        64.18        22.09 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-ZQ-A9CR 
       40.08        32.94        17.13         0.79 

$`16Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4184 
       26.70        11.70        19.56        11.01         9.47         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         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-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       12.82        24.76        23.93        18.15        15.32        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 
        9.07        12.76        17.49        14.43        12.26        20.55 
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 
       19.50        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        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       15.85         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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44         9.86        15.68        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         8.98        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL 
        0.66        19.36        13.51         0.46        20.42        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8527 TCGA-CD-8528 
        5.13         2.83         3.25        13.18         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        11.31        11.61         6.58         0.10        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-4460 TCGA-CG-4462 TCGA-CG-4465 
       54.08         4.01        14.01        21.99         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.36        12.66        19.13        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       17.85        13.35        10.26        15.98        10.55        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-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 
       14.76        13.71        11.24        11.44         9.76         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 
        7.40         7.13         0.62         7.99        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-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       59.54         5.03        13.58         0.56         5.52         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       18.08        26.47         1.51        14.27        14.17        11.41 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62        24.30         5.59        12.30        11.84        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-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 
        6.51        10.19         2.10        12.95        19.36         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.81        21.21         3.45        18.81         3.39         5.36 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        5.19         1.41         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-MX-A5UG 
        5.56         1.81         7.82        13.51         2.53         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73         9.86        45.67        18.21         8.52        61.25 
TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60         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-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
       16.87        19.04         0.92        13.25        13.02        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       16.31         2.50         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       26.24        14.33        65.16        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 
       18.74        20.81         1.71        36.16         7.36         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-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       11.24        18.41        28.41        29.98        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        21.11        12.43        10.62 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.00 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             72.23             122.30 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             12.69              12.92 
[1] "0.1 - 72.2 (12.7)"  "0.0 - 122.3 (12.9)"
[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       10       12        10        13
  16Q LOSS WILD-TYPE       2        9       31       19        28        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           1         30         14         10        6
  16Q LOSS WILD-TYPE         3         55         48         31       40
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  5                  9
  STAGE IB                 10                 31
  STAGE II                 12                 19
  STAGE IIA                10                 28
  STAGE IIB                13                 42
  STAGE III                 1                  3
  STAGE IIIA               30                 55
  STAGE IIIB               14                 48
  STAGE IIIC               10                 31
  STAGE IV                  6                 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
  16Q LOSS MUTATED     7  22  57  27
  16Q LOSS WILD-TYPE  15  68 138  92
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                7                 15
  T2               22                 68
  T3               57                138
  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
  16Q LOSS MUTATED   35 33 20 22
  16Q LOSS WILD-TYPE 94 85 64 67
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               35                 94
  N1               33                 85
  N2               20                 64
  N3               22                 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"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   109   3
  16Q LOSS WILD-TYPE 278  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    109    3
  16Q LOSS WILD-TYPE  278   27
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              109                278
  1                3                 27
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    44  70
  16Q LOSS WILD-TYPE 114 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     44   70
  16Q LOSS WILD-TYPE  114  208
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               44                114
  MALE                 70                208
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16Q LOSS MUTATED                                      13
  16Q LOSS WILD-TYPE                                    58
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                       34
  16Q LOSS WILD-TYPE                                                    128
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                                  20
  16Q LOSS WILD-TYPE                                                                61
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  16Q LOSS MUTATED                                                 30
  16Q LOSS WILD-TYPE                                               48
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16Q LOSS MUTATED                                                          9
  16Q LOSS WILD-TYPE                                                       12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  16Q LOSS MUTATED                                                           3
  16Q LOSS WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16Q LOSS MUTATED                                          4
  16Q LOSS WILD-TYPE                                        9
D70V8, multiclass
                                                                   clus
vv                                                                  16Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         4
                                                                   clus
vv                                                                  16Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           9
[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"
D70V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3 111
  16Q LOSS WILD-TYPE   3 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3  111
  16Q LOSS WILD-TYPE    3  319
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 3                  3
  YES              111                319
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    93   5   4   4
  16Q LOSS WILD-TYPE 254  13  15  21
D70V10, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               93                254
  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      26                         4
  16Q LOSS WILD-TYPE    62                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           0    66
  16Q LOSS WILD-TYPE                                         1   208
D70V12, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                                   26                 62
  BLACK OR AFRICAN AMERICAN                                4                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   66                208
[1] 4 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     0  75
  16Q LOSS WILD-TYPE   4 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0   75
  16Q LOSS WILD-TYPE    4  238
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               75                238
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    95  59
  17P LOSS WILD-TYPE 159  91
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               154                250 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                59                 91 
$`17P LOSS MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 
       11.70        11.01         9.44         6.61         6.18        17.29 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       19.33         9.17        12.16         9.21        35.24        15.42 
TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 
       28.73        18.71         0.69         9.60        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 
       16.31        15.58        13.08        14.04        14.79         5.39 
TCGA-BR-8484 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U 
       25.18        11.54        16.44         9.86        10.68        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD 
        7.53        22.26         1.48         0.72        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 
       20.42         1.15         3.25        13.15         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
        0.07         0.10         0.13         0.13         0.13         3.42 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       11.31        12.43        11.61        12.20        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       27.02         7.99         8.05        54.08         4.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5725 
       47.05        19.07         7.07        30.97         1.02        15.02 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       79.07         4.01        69.04        11.93        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.54        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6820 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A 
       11.31        14.66        16.44        11.31        15.65         7.40 
TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A8CX 
        7.99        11.38        14.07        17.06        13.58         0.23 
TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GH 
        1.51        12.59        14.17        12.10        22.75        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-7806 
        8.98         6.25         2.10        12.95        12.30        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RS 
       18.81         3.39        18.38         5.19         1.41        12.59 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 
        1.81         7.82         2.53         5.56        37.64         9.86 
TCGA-R5-A7O7 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
       45.67         9.24         8.61        16.67       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        5.79         0.92         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       35.24         7.73        46.26        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
        1.87        13.35        27.35        64.57        14.33        65.16 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A92D TCGA-VQ-A94T 
       18.74        20.81        36.16         9.50        64.18        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       22.09        18.41        40.08        29.98        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       16.14        21.11        12.43         0.79 

$`17P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        19.56         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.87        13.68        39.12        26.10        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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
       32.94        12.82        24.76        23.93        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       15.32        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44        12.26        20.55         8.05         0.56 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        19.50         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-8485 TCGA-BR-8486 
       19.17         0.26        15.85         3.72         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
        7.53         0.49        15.81        15.68         8.22        12.56 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI 
        0.53        12.82         0.66        19.36         0.46        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13         2.83        13.18         0.30         0.07 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 
        0.07         0.16         0.10         0.10         0.10         9.34 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 
        6.58         0.10        12.62        15.95         1.02        14.01 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 
       12.03        21.99         0.00         9.01        18.97        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       22.98         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
      105.07        12.03        28.96        65.10        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 
       12.36        12.66        19.13        18.61        17.85        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       18.21        21.14        20.91        14.27         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
        2.96         8.38         4.34         7.13         0.62        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       14.47        72.23        21.27         3.48        19.53        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
       59.54         5.03         0.56         5.52        18.08        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        14.27        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20         3.25        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        10.19         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       19.36        23.84         9.67         8.88         8.81        27.42 
TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR 
        3.45         5.36        13.08         6.44         6.74         6.51 
TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        13.51        60.56        20.15         3.72        19.73 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS 
       18.21         8.52        61.25         6.08         4.60        11.05 
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-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8E3 
       57.44        35.61        16.87        19.04        48.79        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       34.45        27.88        32.48        28.96        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       22.19         2.50         9.27        23.41        15.65        26.24 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U 
       36.69        11.70        11.93        61.22        22.68         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        7.36         9.73        52.24         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-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-ZA-A8F6 
       28.41        32.94        17.13        10.62 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.07               0.00 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            115.69             122.30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            12.690             12.855 
[1] "0.1 - 115.7 (12.7)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         1        6       15       14        14        21
  17P LOSS WILD-TYPE       2        8       26       17        24        34
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           0         33         26         11       17
  17P LOSS WILD-TYPE         4         52         36         30       29
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  6                  8
  STAGE IB                 15                 26
  STAGE II                 14                 17
  STAGE IIA                14                 24
  STAGE IIB                21                 34
  STAGE III                 0                  4
  STAGE IIIA               33                 52
  STAGE IIIB               26                 36
  STAGE IIIC               11                 30
  STAGE IV                 17                 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
  17P LOSS MUTATED     7  37  78  37
  17P LOSS WILD-TYPE  15  53 117  82
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                7                 15
  T2               37                 53
  T3               78                117
  T4               37                 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"
                    vv
clus                 N0 N1 N2 N3
  17P LOSS MUTATED   50 40 35 32
  17P LOSS WILD-TYPE 79 78 49 57
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               50                 79
  N1               40                 78
  N2               35                 49
  N3               32                 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   144   9
  17P LOSS WILD-TYPE 243  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    144    9
  17P LOSS WILD-TYPE  243   21
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              144                243
  1                9                 21
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    49 112
  17P LOSS WILD-TYPE 109 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     49  112
  17P LOSS WILD-TYPE  109  166
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               49                109
  MALE                112                166
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17P LOSS MUTATED                                      15
  17P LOSS WILD-TYPE                                    56
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                       52
  17P LOSS WILD-TYPE                                                    110
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                                  40
  17P LOSS WILD-TYPE                                                                41
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  17P LOSS MUTATED                                                 33
  17P LOSS WILD-TYPE                                               45
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17P LOSS MUTATED                                                         10
  17P LOSS WILD-TYPE                                                       11
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  17P LOSS MUTATED                                                           4
  17P LOSS WILD-TYPE                                                         4
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17P LOSS MUTATED                                          7
  17P LOSS WILD-TYPE                                        6
D71V8, multiclass
                                                                   clus
vv                                                                  17P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         7
                                                                   clus
vv                                                                  17P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           110
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           6
[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"
D71V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4 157
  17P LOSS WILD-TYPE   2 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  157
  17P LOSS WILD-TYPE    2  273
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 4                  2
  YES              157                273
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   129   9   6   5
  17P LOSS WILD-TYPE 218   9  13  20
D71V10, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              129                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                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           1    95
  17P LOSS WILD-TYPE                                         0   179
D71V12, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                                   34                 54
  BLACK OR AFRICAN AMERICAN                                3                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   95                179
[1] 4 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     1 105
  17P LOSS WILD-TYPE   3 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1  105
  17P LOSS WILD-TYPE    3  208
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO              105                208
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    43  27
  17Q LOSS WILD-TYPE 211 123
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                70                334 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                27                123 
$`17Q LOSS MUTATED`
TCGA-B7-A5TJ TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7959 
       11.01        19.33         9.17        35.24        28.73        18.71 
TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8690 
        0.69        16.31        14.79         9.21         9.86        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
        7.53        22.26         0.72        13.51        20.65         1.15 
TCGA-CD-5799 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-A489 TCGA-CD-A48C 
        3.25         0.07         0.10         0.13        11.31        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 
       12.20        20.02         3.02        54.08         4.01        47.05 
TCGA-CG-4449 TCGA-CG-4477 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 
       19.07        30.97        11.93        20.55        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-EQ-8122 
       15.22        11.31        14.66        11.31        15.65         7.99 
TCGA-FP-A8CX TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-IN-8663 
        0.23        12.59        14.17        22.75         8.98         3.39 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A7C1 
        5.56        37.64         9.86        45.67         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PH 
      115.69         8.94         5.79         5.46        46.26        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y 
       17.85         1.87        64.57        18.74         9.50         9.73 
TCGA-VQ-A94U TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       22.09        29.98        21.11         0.79 

$`17Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       12.76        17.49        14.43        11.44        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       20.55         8.05         0.56        12.95         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        19.50        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-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        19.17         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44        15.68         8.22        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        13.41        13.51        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        12.82         0.66        19.36         0.46 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
       20.42        13.64        11.57         5.13         2.83        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        3.42         9.34        12.43         6.58         0.10        12.62 
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-4443 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        22.98         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        7.99        12.36        12.66        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85        13.35        15.98        12.79        10.55 
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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        2.96         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        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-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58         0.56         5.52        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        14.27        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        12.30         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21         3.45        18.81        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.08         1.41         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
        5.56         1.81         7.82        13.51         2.53        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       20.15         3.72        19.73        18.21         8.52        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
        6.08         4.60         9.24        11.05         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       37.91        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87        19.04         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        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        28.96        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        2.70         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       27.35        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        20.81        22.68         1.71        36.16         7.36 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       52.24         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        64.18        21.04         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        40.08        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        12.43        10.62 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.07               0.00 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            115.69             122.30 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            12.065             12.950 
[1] "0.1 - 115.7 (12.1)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         0        1        5        6         5        12
  17Q LOSS WILD-TYPE       3       13       36       25        33        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           0         17         14          4        7
  17Q LOSS WILD-TYPE         4         68         48         37       39
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  1                 13
  STAGE IB                  5                 36
  STAGE II                  6                 25
  STAGE IIA                 5                 33
  STAGE IIB                12                 43
  STAGE III                 0                  4
  STAGE IIIA               17                 68
  STAGE IIIB               14                 48
  STAGE IIIC                4                 37
  STAGE IV                  7                 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
  17Q LOSS MUTATED     1  15  34  22
  17Q LOSS WILD-TYPE  21  75 161  97
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                1                 21
  T2               15                 75
  T3               34                161
  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
  17Q LOSS MUTATED    17  22  18  14
  17Q LOSS WILD-TYPE 112  96  66  75
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               17                112
  N1               22                 96
  N2               18                 66
  N3               14                 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"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    67   3
  17Q LOSS WILD-TYPE 320  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     67    3
  17Q LOSS WILD-TYPE  320   27
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               67                320
  1                3                 27
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    28  46
  17Q LOSS WILD-TYPE 130 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     28   46
  17Q LOSS WILD-TYPE  130  232
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               28                130
  MALE                 46                232
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17Q LOSS MUTATED                                       7
  17Q LOSS WILD-TYPE                                    64
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                       22
  17Q LOSS WILD-TYPE                                                    140
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                                  18
  17Q LOSS WILD-TYPE                                                                63
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  17Q LOSS MUTATED                                                 17
  17Q LOSS WILD-TYPE                                               61
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17Q LOSS MUTATED                                                          4
  17Q LOSS WILD-TYPE                                                       17
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  17Q LOSS MUTATED                                                           2
  17Q LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17Q LOSS MUTATED                                          4
  17Q LOSS WILD-TYPE                                        9
D72V8, multiclass
                                                                   clus
vv                                                                  17Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         4
                                                                   clus
vv                                                                  17Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           9
[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"
D72V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  73
  17Q LOSS WILD-TYPE   5 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   73
  17Q LOSS WILD-TYPE    5  357
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                  5
  YES               73                357
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    57   3   4   3
  17Q LOSS WILD-TYPE 290  15  15  22
D72V10, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               57                290
  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      15                         1
  17Q LOSS WILD-TYPE    73                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           1    46
  17Q LOSS WILD-TYPE                                         0   228
D72V12, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                1                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   46                228
[1] 4 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   3 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   51
  17Q LOSS WILD-TYPE    3  262
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               51                262
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    78  33
  18P LOSS WILD-TYPE 176 117
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               111                293 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                33                117 
$`18P LOSS MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4279 TCGA-BR-6456 
       19.56        11.01         9.47         9.44         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        15.42        28.01 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8366 
       28.73         9.07         2.66        16.31        22.19         0.95 
TCGA-BR-8369 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 
       14.04        25.18        15.81         0.49        11.54         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       15.68        10.68        13.87         7.53        22.26         1.48 
TCGA-BR-A4IY TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       12.89        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         0.10         0.13        11.31        12.43 
TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 
       11.61         7.99         8.05        54.08         4.01        47.05 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 TCGA-D7-6518 TCGA-D7-6519 
       19.07         7.07        30.97         1.02        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        15.16        11.24         9.76         0.62        72.23 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-A8CX 
       11.38        19.53        14.07        22.29        17.06         0.23 
TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G6 
        1.51        12.59        14.17        12.10        10.62        12.30 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 
       11.77         8.98         6.25         2.10        12.95         9.67 
TCGA-IN-A6RL TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H 
        5.19         1.81        13.51         5.56        20.15        37.64 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-SW-A7EB 
       45.67        18.21         8.52        16.67       115.69         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PD 
       48.79         5.46        13.02        18.48        35.24        16.31 
TCGA-VQ-A8PF TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R 
        2.50        36.16        52.24         4.54        64.18        42.54 
TCGA-VQ-A94U TCGA-VQ-AA6B TCGA-VQ-AA6K 
       22.09        29.98        12.43 

$`18P LOSS WILD-TYPE`
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-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.87        19.33        39.12         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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
       32.94        12.82         9.21        24.76        23.93        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        12.43         3.45        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        12.95         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 
        6.18        19.50        13.08         0.26        17.52        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       15.85         3.72         5.39         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 
       12.79         9.34        13.45         6.28         7.53        15.81 
TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       16.44         8.22        12.56         6.08        13.41        13.51 
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        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        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 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 
        0.30         0.07         0.16         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        3.42         9.34         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 
       20.02         3.02        27.02        15.95         1.02        14.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       12.00        22.98         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-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       12.66        11.93        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        10.55        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        13.71        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        2.96        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 
        7.99        16.24        14.47        21.27         3.48        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         5.52        18.08        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
        5.92        14.27        11.41         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        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        10.19         0.26        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         8.88         8.81        27.42        21.21 
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         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        1.41         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        7.82         2.53        60.56         3.72        19.73         9.86 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         6.08         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-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-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       28.96        34.29        46.26        22.19        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 
        1.71         7.36         9.50         9.73         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T 
       55.43         6.58         5.72        21.04         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        40.08        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        21.11        10.62         0.79 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.00 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            115.69             122.30 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             12.95              12.79 
[1] "0.1 - 115.7 (12.9)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         0        3        7       10        13        14
  18P LOSS WILD-TYPE       3       11       34       21        25        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED           0         28         17         10       12
  18P LOSS WILD-TYPE         4         57         45         31       34
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  3                 11
  STAGE IB                  7                 34
  STAGE II                 10                 21
  STAGE IIA                13                 25
  STAGE IIB                14                 41
  STAGE III                 0                  4
  STAGE IIIA               28                 57
  STAGE IIIB               17                 45
  STAGE IIIC               10                 31
  STAGE IV                 12                 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
  18P LOSS MUTATED     2  22  61  30
  18P LOSS WILD-TYPE  20  68 134  89
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                2                 20
  T2               22                 68
  T3               61                134
  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   33 28 26 26
  18P LOSS WILD-TYPE 96 90 58 63
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               33                 96
  N1               28                 90
  N2               26                 58
  N3               26                 63
[1] 4 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   104   9
  18P LOSS WILD-TYPE 283  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    104    9
  18P LOSS WILD-TYPE  283   21
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              104                283
  1                9                 21
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    34  83
  18P LOSS WILD-TYPE 124 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     34   83
  18P LOSS WILD-TYPE  124  195
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               34                124
  MALE                 83                195
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18P LOSS MUTATED                                      20
  18P LOSS WILD-TYPE                                    51
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                       40
  18P LOSS WILD-TYPE                                                    122
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                                  20
  18P LOSS WILD-TYPE                                                                61
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  18P LOSS MUTATED                                                 25
  18P LOSS WILD-TYPE                                               53
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18P LOSS MUTATED                                                          5
  18P LOSS WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  18P LOSS MUTATED                                                           2
  18P LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18P LOSS MUTATED                                          5
  18P LOSS WILD-TYPE                                        8
D73V8, multiclass
                                                                   clus
vv                                                                  18P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         5
                                                                   clus
vv                                                                  18P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[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"
D73V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     0 117
  18P LOSS WILD-TYPE   6 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0  117
  18P LOSS WILD-TYPE    6  313
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 0                  6
  YES              117                313
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    91   5   4   5
  18P LOSS WILD-TYPE 256  13  15  20
D73V10, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               91                256
  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"
D73V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED      33                         4
  18P LOSS WILD-TYPE    55                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           0    67
  18P LOSS WILD-TYPE                                         1   207
D73V12, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                                   33                 55
  BLACK OR AFRICAN AMERICAN                                4                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   67                207
[1] 4 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     2  88
  18P LOSS WILD-TYPE   2 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   88
  18P LOSS WILD-TYPE    2  225
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               88                225
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    97  48
  18Q LOSS WILD-TYPE 157 102
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               145                259 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                48                102 
$`18Q LOSS MUTATED`
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-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6709 
        6.18         9.57        17.29        13.68        26.10        12.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8060 
       35.24        15.42        28.01        28.73         9.07        11.44 
TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8486 
       16.31        22.19         0.95        14.04         3.32        20.22 
TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       15.81         0.49        11.54         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J6 
       10.68        13.87         7.53        22.26        12.89         0.66 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 
        0.07         0.10         0.13         0.10         0.13         3.42 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 
       12.43        11.61        12.20         3.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4469 
       54.08         4.01        47.05        19.07        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5577 
       22.98        30.97         1.02        12.03         4.01        12.36 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       19.13        20.55        18.54        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU 
       15.98        19.50        18.21        14.66        21.14        16.44 
TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
       15.16        11.24         9.76         2.96        15.65         7.40 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 
        0.62         7.99        72.23        11.38        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       22.29        17.06         0.23        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 
       10.62        12.30        11.77         8.98         6.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NT 
       12.95         9.67         5.19         1.41         6.74         5.56 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
        1.81        13.51         5.56        60.56        20.15        37.64 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-SW-A7EB 
       45.67        18.21        16.67        37.91       115.69         5.79 
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        35.24 
TCGA-VQ-A8P5 TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PS 
        7.73        16.31        22.19         2.50        17.85        13.35 
TCGA-VQ-A8PU TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A925 
       27.35        36.16         9.50        52.24         2.01         4.54 
TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6B 
       64.18        42.54        11.24        22.09        32.94        29.98 
TCGA-VQ-AA6K 
       12.43 

$`18Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       26.70         6.97         4.64         7.43        18.35        30.90 
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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       24.76        23.93        18.15        15.32        12.43         3.45 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         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        19.50        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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         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        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS 
        7.53        15.81        16.44        12.56         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         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 
       12.82        19.36        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        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       13.15         0.16         0.10         0.13         0.10         9.34 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
       11.31         6.58         0.10        12.62        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4460 
       15.95         1.02        14.01        29.98        12.03        21.99 
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-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
       65.10        69.04        21.07         7.99        12.66        11.93 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       18.84        18.61        17.85        15.22        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 
       11.31        12.33        24.72        16.80        17.19        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
       14.27         5.92        13.78        14.76        13.71        11.31 
TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
       11.44         8.38         4.34         7.13        16.24        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       21.27         3.48        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        5.52        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       11.41         0.76        24.30         5.59        11.84        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-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.51        10.19         0.26        19.36        23.84        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        8.88         8.81        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
        3.39        18.38         5.36        13.08         6.44        12.59 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        6.51         7.82         2.53         3.72        19.73         9.86 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
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-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-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        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        26.24        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
        1.71         7.36         9.73         9.04        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        5.72        21.04         2.66        18.41        40.08        28.41 
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        21.11        10.62 
TCGA-ZQ-A9CR 
        0.79 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.00 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            115.69             122.30 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             12.43              13.08 
[1] "0.1 - 115.7 (12.4)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         0        5       14       12        16        17
  18Q LOSS WILD-TYPE       3        9       27       19        22        38
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED           0         37         24         11       13
  18Q LOSS WILD-TYPE         4         48         38         30       33
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  5                  9
  STAGE IB                 14                 27
  STAGE II                 12                 19
  STAGE IIA                16                 22
  STAGE IIB                17                 38
  STAGE III                 0                  4
  STAGE IIIA               37                 48
  STAGE IIIB               24                 38
  STAGE IIIC               11                 30
  STAGE IV                 13                 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
  18Q LOSS MUTATED     5  32  84  30
  18Q LOSS WILD-TYPE  17  58 111  89
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                5                 17
  T2               32                 58
  T3               84                111
  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 40 32 31
  18Q LOSS WILD-TYPE 84 78 52 58
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               45                 84
  N1               40                 78
  N2               32                 52
  N3               31                 58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   137  10
  18Q LOSS WILD-TYPE 250  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    137   10
  18Q LOSS WILD-TYPE  250   20
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              137                250
  1               10                 20
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    52 101
  18Q LOSS WILD-TYPE 106 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     52  101
  18Q LOSS WILD-TYPE  106  177
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               52                106
  MALE                101                177
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18Q LOSS MUTATED                                      23
  18Q LOSS WILD-TYPE                                    48
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                       53
  18Q LOSS WILD-TYPE                                                    109
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                                  32
  18Q LOSS WILD-TYPE                                                                49
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  18Q LOSS MUTATED                                                 31
  18Q LOSS WILD-TYPE                                               47
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18Q LOSS MUTATED                                                          5
  18Q LOSS WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  18Q LOSS MUTATED                                                           3
  18Q LOSS WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18Q LOSS MUTATED                                          5
  18Q LOSS WILD-TYPE                                        8
D74V8, multiclass
                                                                   clus
vv                                                                  18Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          53
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         5
                                                                   clus
vv                                                                  18Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           109
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 49
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[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"
D74V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1 152
  18Q LOSS WILD-TYPE   5 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1  152
  18Q LOSS WILD-TYPE    5  278
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 1                  5
  YES              152                278
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   117   7   7   8
  18Q LOSS WILD-TYPE 230  11  12  17
D74V10, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              117                230
  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      36                         3
  18Q LOSS WILD-TYPE    52                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           0    93
  18Q LOSS WILD-TYPE                                         1   181
D74V12, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                                   36                 52
  BLACK OR AFRICAN AMERICAN                                3                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   93                181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V13, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     2 107
  18Q LOSS WILD-TYPE   2 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2  107
  18Q LOSS WILD-TYPE    2  206
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO              107                206
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    59  49
  19P LOSS WILD-TYPE 195 101
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               108                296 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                49                101 
$`19P LOSS MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6565 TCGA-BR-7704 
       19.56        11.01         9.44         6.61         9.17        35.24 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 
       28.01        28.73         3.45        11.44         0.69         2.66 
TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8690 
        2.20        14.04        14.79         9.21        11.54        10.68 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 
       22.26         1.48         0.72        20.65         1.15         3.25 
TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A489 
       13.15         0.07         0.07         0.07         3.42        11.31 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       12.43        12.20        20.02         7.99        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6520 
       29.98        18.97        12.03        15.02        69.04        18.84 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A6EX 
       13.35        10.26        12.79        11.31        19.50        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7916 
        2.96        15.65         0.62         7.99        72.23        14.07 
TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP 
       17.06         0.56         5.92        12.59        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        6.25         2.10        23.84        12.30         9.67        27.42 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        3.39        18.38         1.41        12.59         5.56         1.81 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        5.56        60.56        37.64        45.67        18.21         6.08 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.61         5.13        37.91         8.94         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 
        5.46        13.25        13.02        18.48        35.24         7.73 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        27.35        18.74         1.71        36.16 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A94O 
        9.50         9.73        52.24         9.04         2.01        21.04 
TCGA-VQ-AA68 TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       40.08        17.13        16.14        21.11        12.43         0.79 

$`19P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        23.93        15.42        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31        15.58         7.40         6.18        19.50        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        19.17         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68         8.22        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        7.53         6.08        13.41        13.51        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        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42        13.64        11.57         5.13         2.83 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
       13.18         0.30         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        9.34        11.61         6.58         0.10        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4444 
       27.02        15.95         1.02         8.05        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       19.07        12.03        21.99         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        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-5727 
        0.99         6.02         0.99       105.07        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        20.55        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       17.19        15.22        15.98        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       13.71        11.24        11.44         9.76         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.40         7.13        16.24        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-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
        5.52         0.23        18.08        26.47         1.51        14.27 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        21.37        29.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        0.26        12.95        19.36         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.45        18.81         5.36         5.19        13.08         6.44 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93G 
        6.74         6.51         7.82        13.51         2.53        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
        3.72        19.73         9.86         8.52        61.25         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
        9.24        11.05        16.67       122.30        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-SW-A7EB TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
        5.79        21.73        34.45        27.88        32.48        28.96 
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-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        2.70         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A925 
       61.22        20.81        22.68         7.36        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        64.18         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       22.09        18.41        28.41        32.94        29.98        54.12 
TCGA-VQ-AA6G TCGA-ZA-A8F6 
       26.04        10.62 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.07               0.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             72.23             122.30 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            11.655             13.430 
[1] "0.1 - 72.2 (11.7)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         1        5       10        6        11        14
  19P LOSS WILD-TYPE       2        9       31       25        27        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           1         26         13         13       12
  19P LOSS WILD-TYPE         3         59         49         28       34
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  5                  9
  STAGE IB                 10                 31
  STAGE II                  6                 25
  STAGE IIA                11                 27
  STAGE IIB                14                 41
  STAGE III                 1                  3
  STAGE IIIA               26                 59
  STAGE IIIB               13                 49
  STAGE IIIC               13                 28
  STAGE IV                 12                 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
  19P LOSS MUTATED     6  23  51  32
  19P LOSS WILD-TYPE  16  67 144  87
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                6                 16
  T2               23                 67
  T3               51                144
  T4               32                 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"
                    vv
clus                 N0 N1 N2 N3
  19P LOSS MUTATED   31 27 22 29
  19P LOSS WILD-TYPE 98 91 62 60
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               31                 98
  N1               27                 91
  N2               22                 62
  N3               29                 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"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   103   6
  19P LOSS WILD-TYPE 284  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    103    6
  19P LOSS WILD-TYPE  284   24
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0              103                284
  1                6                 24
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    40  74
  19P LOSS WILD-TYPE 118 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     40   74
  19P LOSS WILD-TYPE  118  204
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               40                118
  MALE                 74                204
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19P LOSS MUTATED                                      10
  19P LOSS WILD-TYPE                                    61
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                       37
  19P LOSS WILD-TYPE                                                    125
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                                  32
  19P LOSS WILD-TYPE                                                                49
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  19P LOSS MUTATED                                                 27
  19P LOSS WILD-TYPE                                               51
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19P LOSS MUTATED                                                          1
  19P LOSS WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  19P LOSS MUTATED                                                           4
  19P LOSS WILD-TYPE                                                         4
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19P LOSS MUTATED                                          3
  19P LOSS WILD-TYPE                                       10
D75V8, multiclass
                                                                   clus
vv                                                                  19P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          37
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  19P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 49
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          10
[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"
D75V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2 112
  19P LOSS WILD-TYPE   4 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2  112
  19P LOSS WILD-TYPE    4  318
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 2                  4
  YES              112                318
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    90   2   6   3
  19P LOSS WILD-TYPE 257  16  13  22
D75V10, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               90                257
  R1                2                 16
  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"
D75V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED      26                         6
  19P LOSS WILD-TYPE    62                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           1    63
  19P LOSS WILD-TYPE                                         0   211
D75V12, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                                   26                 62
  BLACK OR AFRICAN AMERICAN                                6                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   63                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"
D75V13, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1  74
  19P LOSS WILD-TYPE   3 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   74
  19P LOSS WILD-TYPE    3  239
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               74                239
[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 204 118
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                82                322 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                32                118 
$`19Q LOSS MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7723 
       11.01         9.44         6.61         9.17        35.24        28.73 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 
       11.44         0.69         2.66         2.20        14.04        14.79 
TCGA-BR-8678 TCGA-BR-A4CS TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 
       11.54         1.48        20.65         1.15         3.25        13.15 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
        0.07         0.07         3.42        11.31        12.43        12.20 
TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4466 
       20.02         7.99         4.01        29.98        19.07        18.97 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       12.03        15.02        69.04        10.26        15.22        12.79 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 
       11.31        19.50        11.31         2.96        15.65         0.62 
TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP 
       17.06         0.56         5.92        12.59        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI 
        6.25        23.84        12.30         9.67        27.42        18.38 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
        1.41        12.59         5.56         1.81         5.56        37.64 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BW TCGA-RD-A8MW TCGA-VQ-A8DT TCGA-VQ-A8DU 
       45.67        18.21         5.13        37.91        48.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU 
       13.02        18.48        35.24        17.85         1.87        27.35 
TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O 
       18.74        36.16         9.50        52.24         9.04        21.04 
TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       17.13        16.14        21.11         0.79 

$`19Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        12.95        16.31        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        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        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        22.26        13.41        13.51        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        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.42        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
        2.83        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        0.13         0.10         9.34        11.61         6.58         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       12.62         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       54.08        14.01        47.05        12.03        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01         7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        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 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 
       18.54        18.61        17.85        13.35        17.19        15.98 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       10.55        12.33        24.72        16.80        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 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
        9.76         8.38         4.34         7.40         7.13         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        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-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
        5.52         0.23        18.08        26.47         1.51        14.27 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        21.37        29.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26         2.10        12.95        19.36         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21         3.45        18.81         3.39         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
       13.08         6.44         6.74         6.51         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53        60.56        20.15         3.72        19.73         9.86 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        8.61        16.67       122.30        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-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.79         0.92        13.25        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       22.19         2.50        12.79         2.70         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        26.24        64.57        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       36.69        11.70        11.93        61.22        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        1.71         7.36         9.73         2.01        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        64.18         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       22.09        18.41        40.08        28.41        32.94        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        12.43        10.62 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             69.04             122.30 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             12.25              13.08 
[1] "0.1 - 69.0 (12.2)"  "0.0 - 122.3 (13.1)"
[1] "hr=" "1.2"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         1        4        9        6         9        10
  19Q LOSS WILD-TYPE       2       10       32       25        29        45
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           0         18         12          6       10
  19Q LOSS WILD-TYPE         4         67         50         35       36
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  4                 10
  STAGE IB                  9                 32
  STAGE II                  6                 25
  STAGE IIA                 9                 29
  STAGE IIB                10                 45
  STAGE III                 0                  4
  STAGE IIIA               18                 67
  STAGE IIIB               12                 50
  STAGE IIIC                6                 35
  STAGE IV                 10                 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 LOSS MUTATED     5  19  39  22
  19Q LOSS WILD-TYPE  17  71 156  97
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                5                 17
  T2               19                 71
  T3               39                156
  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  20
  19Q LOSS WILD-TYPE 102  99  67  69
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               27                102
  N1               19                 99
  N2               17                 67
  N3               20                 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    78   6
  19Q LOSS WILD-TYPE 309  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     78    6
  19Q LOSS WILD-TYPE  309   24
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               78                309
  1                6                 24
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    31  56
  19Q LOSS WILD-TYPE 127 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     31   56
  19Q LOSS WILD-TYPE  127  222
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               31                127
  MALE                 56                222
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19Q LOSS MUTATED                                       6
  19Q LOSS WILD-TYPE                                    65
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                       28
  19Q LOSS WILD-TYPE                                                    134
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                                  23
  19Q LOSS WILD-TYPE                                                                58
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  19Q LOSS MUTATED                                                 22
  19Q LOSS WILD-TYPE                                               56
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19Q LOSS MUTATED                                                          2
  19Q LOSS WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  19Q LOSS MUTATED                                                           4
  19Q LOSS WILD-TYPE                                                         4
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19Q LOSS MUTATED                                          2
  19Q LOSS WILD-TYPE                                       11
D76V8, multiclass
                                                                   clus
vv                                                                  19Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                22
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  19Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  56
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          11
[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"
D76V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  86
  19Q LOSS WILD-TYPE   5 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   86
  19Q LOSS WILD-TYPE    5  344
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 1                  5
  YES               86                344
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    71   0   4   3
  19Q LOSS WILD-TYPE 276  18  15  22
D76V10, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               71                276
  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                         4
  19Q LOSS WILD-TYPE    67                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           0    46
  19Q LOSS WILD-TYPE                                         1   228
D76V12, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                                   21                 67
  BLACK OR AFRICAN AMERICAN                                4                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   46                228
[1] 4 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  57
  19Q LOSS WILD-TYPE   3 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   57
  19Q LOSS WILD-TYPE    3  256
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               57                256
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     9  11
  20P LOSS WILD-TYPE 245 139
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                20                384 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                11                139 
$`20P LOSS MUTATED`
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-8289 TCGA-BR-A4PD TCGA-CG-4301 
        6.18        17.29        26.10         2.66        20.65         3.02 
TCGA-D7-6519 TCGA-D7-8575 TCGA-D7-8576 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-HU-8249 
       20.55        18.21        14.66         0.62        16.24        14.17 
TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-AB1V TCGA-IP-7968 TCGA-VQ-A8DU TCGA-VQ-A8E0 
        5.36         1.41         7.82         2.53         5.46        18.48 
TCGA-VQ-A8PY TCGA-VQ-AA68 
       14.33        40.08 

$`20P LOSS WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        12.95        16.31         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        19.50        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 
       19.17        14.79         0.26        15.85         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        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        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        12.82         0.66        19.36        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        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62        20.02        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       18.97         7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        79.07        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        12.36        12.66        11.93 
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        10.55 
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-D7-8578 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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
        9.76         2.96        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         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-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        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         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.30         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38         5.19        13.08 
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         5.56         1.81 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
       13.51         5.56        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73         9.86        45.67        18.21         8.52        61.25 
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        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
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-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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        26.24        27.35        64.57        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        36.16         7.36         9.50         9.73        52.24 
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-A94U 
       64.18        21.04         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        28.41        32.94        29.98        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        21.11        12.43        10.62         0.79 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.62               0.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             40.08             122.30 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            14.250             12.805 
[1] "0.6 - 40.1 (14.2)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.9"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         0        2        3        0         0         2
  20P LOSS WILD-TYPE       3       12       38       31        38        53
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           0          5          5          1        4
  20P LOSS WILD-TYPE         4         80         57         40       42
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   0                  3
  STAGE IA                  2                 12
  STAGE IB                  3                 38
  STAGE II                  0                 31
  STAGE IIA                 0                 38
  STAGE IIB                 2                 53
  STAGE III                 0                  4
  STAGE IIIA                5                 80
  STAGE IIIB                5                 57
  STAGE IIIC                1                 40
  STAGE IV                  4                 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
  20P LOSS MUTATED     3   4   9   6
  20P LOSS WILD-TYPE  19  86 186 113
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                3                 19
  T2                4                 86
  T3                9                186
  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 123 114  77  84
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                6                123
  N1                4                114
  N2                7                 77
  N3                5                 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"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    16   3
  20P LOSS WILD-TYPE 371  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     16    3
  20P LOSS WILD-TYPE  371   27
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               16                371
  1                3                 27
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    11  11
  20P LOSS WILD-TYPE 147 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     11   11
  20P LOSS WILD-TYPE  147  267
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               11                147
  MALE                 11                267
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  20P LOSS MUTATED                                       2
  20P LOSS WILD-TYPE                                    69
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                       11
  20P LOSS WILD-TYPE                                                    151
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                                   2
  20P LOSS WILD-TYPE                                                                79
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  20P LOSS MUTATED                                                  6
  20P LOSS WILD-TYPE                                               72
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  20P LOSS MUTATED                                                          1
  20P LOSS WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  20P LOSS MUTATED                                                           0
  20P LOSS WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  20P LOSS MUTATED                                          0
  20P LOSS WILD-TYPE                                       13
D77V8, multiclass
                                                                   clus
vv                                                                  20P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  20P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             69
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           151
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 79
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  72
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          13
[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"
D77V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  20
  20P LOSS WILD-TYPE   4 410
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   20
  20P LOSS WILD-TYPE    4  410
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 2                  4
  YES               20                410
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    18   1   2   1
  20P LOSS WILD-TYPE 329  17  17  24
D77V10, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               18                329
  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                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           0    16
  20P LOSS WILD-TYPE                                         1   258
D77V12, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                                    2                 86
  BLACK OR AFRICAN AMERICAN                                1                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   16                258
[1] 4 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   4 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   15
  20P LOSS WILD-TYPE    4  298
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               15                298
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   102  64
  21Q LOSS WILD-TYPE 152  86
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               166                238 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                64                 86 
$`21Q LOSS MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6457 
       11.70        11.01         9.44         6.97        18.35        13.68 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 
       19.33        26.10         9.17        31.20        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 
       28.01        28.73        18.71        14.43        11.44         9.60 
TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8365 
        8.05        16.31        15.58         7.40        19.50        17.52 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        4.31        14.04        14.79         5.39        25.18         9.21 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ 
       11.54         9.86        15.68        10.68         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        1.48         0.72        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        1.15        13.64         0.07         0.07         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.16         0.13        11.31        12.43        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 
       20.02        54.08         4.01        47.05        12.03        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 
       22.98        30.97         6.97         1.02        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6525 
       65.10         4.01        69.04        11.93        19.13        13.35 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8576 TCGA-D7-8578 
       17.19        15.98        12.79        11.31        14.66        21.14 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 
       16.44        11.31        15.65         7.40         0.62        72.23 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 
       11.38        19.53        17.06         0.23        26.47         1.51 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-A4GU 
       14.17        12.10        11.84         3.25         8.98         6.25 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 
        0.26        19.36        23.84        12.30         9.67        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO 
       18.81         3.39        18.38         5.36         5.19         1.41 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 
        6.74         6.51         5.56         1.81         7.82         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 
        5.56        60.56        20.15        37.64         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A8MV 
       18.21         8.52        61.25         6.08         9.24       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
       37.91       115.69        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PE 
        0.92        48.79        13.25        18.48         7.73        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       17.85         1.87        23.41        27.35        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       36.69        61.22        18.74        20.81         1.71        36.16 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A94O 
        9.73        52.24         2.01        55.43         4.54        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B 
       42.54        11.24        22.09        18.41        40.08        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       54.12        21.11        12.43         0.79 

$`21Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       26.70        19.56         9.47         6.61         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         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        21.11        30.90        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       12.82         9.21        24.76        23.93        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8077 
       12.43         3.45         9.07        12.76        17.49         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       12.26        20.55         0.56        12.95         2.66         2.20 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
        6.18        13.08         0.26        22.19         0.95        26.33 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        19.17         0.26        15.85         3.72 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 
        6.28         7.53         0.49        15.81        16.44         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56        13.87         6.08        13.41        13.51        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        12.82         0.66        19.36 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.30         0.07         0.07         0.13         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI 
        0.13         0.10         3.42         9.34         6.58         0.10 
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-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
        8.05        14.01        29.98        19.07        21.99         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-5727 TCGA-CG-5733 TCGA-CG-5734 
        0.99       105.07        28.96        79.07        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.36        12.66        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       17.85        10.26        15.22        10.55        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        19.50        17.19        18.21        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44         9.76         2.96         8.38         4.34         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 
        7.99        16.24        14.47        21.27         3.48        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-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       18.08         5.92        14.27        12.59        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD 
        0.76        24.30         5.59        12.30        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 
       10.19         2.10        12.95         8.88         8.81        27.42 
TCGA-IN-7808 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-AB1X TCGA-MX-A5UG 
        3.45        13.08         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        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        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        26.24        65.16 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 
       11.70        11.93        22.68         7.36         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        64.18         2.66        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       17.13        26.04        16.14        10.62 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.07               0.00 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            122.30             116.38 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            13.575             12.775 
[1] "0.1 - 122.3 (13.6)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.1"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         1        4       18        8        16        22
  21Q LOSS WILD-TYPE       2       10       23       23        22        33
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           2         43         24         16       17
  21Q LOSS WILD-TYPE         2         42         38         25       29
D78V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  4                 10
  STAGE IB                 18                 23
  STAGE II                  8                 23
  STAGE IIA                16                 22
  STAGE IIB                22                 33
  STAGE III                 2                  2
  STAGE IIIA               43                 42
  STAGE IIIB               24                 38
  STAGE IIIC               16                 25
  STAGE IV                 17                 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
  21Q LOSS MUTATED     6  37  85  44
  21Q LOSS WILD-TYPE  16  53 110  75
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                6                 16
  T2               37                 53
  T3               85                110
  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
  21Q LOSS MUTATED   46 49 40 35
  21Q LOSS WILD-TYPE 83 69 44 54
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               46                 83
  N1               49                 69
  N2               40                 44
  N3               35                 54
[1] 4 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   160   9
  21Q LOSS WILD-TYPE 227  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    160    9
  21Q LOSS WILD-TYPE  227   21
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              160                227
  1                9                 21
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    69 108
  21Q LOSS WILD-TYPE  89 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     69  108
  21Q LOSS WILD-TYPE   89  170
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               69                 89
  MALE                108                170
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  21Q LOSS MUTATED                                      23
  21Q LOSS WILD-TYPE                                    48
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                       62
  21Q LOSS WILD-TYPE                                                    100
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                                  39
  21Q LOSS WILD-TYPE                                                                42
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  21Q LOSS MUTATED                                                 36
  21Q LOSS WILD-TYPE                                               42
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  21Q LOSS MUTATED                                                          9
  21Q LOSS WILD-TYPE                                                       12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  21Q LOSS MUTATED                                                           1
  21Q LOSS WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  21Q LOSS MUTATED                                          6
  21Q LOSS WILD-TYPE                                        7
D78V8, multiclass
                                                                   clus
vv                                                                  21Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          62
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         6
                                                                   clus
vv                                                                  21Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           100
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 42
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[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"
D78V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4 173
  21Q LOSS WILD-TYPE   2 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4  173
  21Q LOSS WILD-TYPE    2  257
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 4                  2
  YES              173                257
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED   144   7   6   8
  21Q LOSS WILD-TYPE 203  11  13  17
D78V10, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              144                203
  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                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           0   111
  21Q LOSS WILD-TYPE                                         1   163
D78V12, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                                   31                 57
  BLACK OR AFRICAN AMERICAN                                6                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  111                163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     2 119
  21Q LOSS WILD-TYPE   2 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2  119
  21Q LOSS WILD-TYPE    2  194
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO              119                194
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    78  54
  22Q LOSS WILD-TYPE 176  96
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               132                272 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                54                 96 
$`22Q LOSS MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 
       11.01         9.44         6.61         6.18        17.29        19.33 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 
       26.10         9.17        12.16         9.21        15.42        28.01 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8297 
       17.49        14.43        11.44         0.69         9.60         7.40 
TCGA-BR-8369 TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
       14.04        25.18         0.49        11.54        16.44         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD 
        8.22        10.68        22.26         0.72        19.36        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 
        1.15        13.64        13.15         0.30         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.07         0.16         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       12.43        11.61        12.20         8.05        54.08         4.01 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5725 
       47.05        21.99        18.97        30.97        12.03        15.02 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 
       69.04        12.66        11.93        20.55        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU 
       12.79        11.31        19.50        18.21        21.14        16.44 
TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-FP-7829 
       11.31        15.65         7.40         0.62        16.24        19.53 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GD 
       17.06         0.56         5.52         5.92        14.17        22.75 
TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD 
        8.98         0.26         2.10        23.84         9.67        27.42 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38         5.36        13.08         6.44         6.74 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A663 
        1.81         7.82         2.53         5.56        20.15         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 
       45.67        18.21         6.08         8.61        16.67       115.69 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK 
       13.02        18.48        46.26        22.19        12.79        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q 
        1.87        27.35        14.33        36.69        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A92D 
        1.71        36.16         9.50         9.73         4.54        64.18 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       11.24        22.09        18.41        32.94        29.98         0.79 

$`22Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        7.43        18.35        30.90         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 
       15.95        13.87        13.68        39.12        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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 
       32.94        12.82        24.76        35.24        23.93        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       18.71        12.26        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         6.18        19.50 
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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       15.85         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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.81        15.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        12.82         0.66        13.51         0.46        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 
       11.57         5.13         2.83         3.25        13.18         0.07 
TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.10         0.13         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.10         6.58         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4443 
       27.02        15.95         1.02         7.99        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       19.07        12.03         0.00         9.01         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        28.96        79.07        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       21.07         7.99        12.36        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6818 
       18.61        17.85        13.35        17.19        15.98        10.55 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 
       12.33        24.72        16.80        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        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.24        11.44         9.76         2.96         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        0.23        18.08        26.47         1.51        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        11.84        24.20         3.25        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         6.25        10.19 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       12.95        19.36        12.30         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR 
        3.45        18.81         5.19         1.41        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        13.51        60.56        37.64         3.72        19.73 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
        8.52        61.25         4.60         9.24        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-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        8.94        16.87        19.04        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       27.88        32.48         7.73        28.96        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.50         2.70         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       26.24        64.57        65.16        11.70        11.93        61.22 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       22.68         7.36        52.24         9.04         2.01        55.43 
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        40.08 
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        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        10.62 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.07               0.00 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            115.69             122.30 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            12.315             13.015 
[1] "0.1 - 115.7 (12.3)" "0.0 - 122.3 (13.0)"
[1] "hr=" "1.3"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         1        1       15       11        11        18
  22Q LOSS WILD-TYPE       2       13       26       20        27        37
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           2         33         22         12       13
  22Q LOSS WILD-TYPE         2         52         40         29       33
D79V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   1                  2
  STAGE IA                  1                 13
  STAGE IB                 15                 26
  STAGE II                 11                 20
  STAGE IIA                11                 27
  STAGE IIB                18                 37
  STAGE III                 2                  2
  STAGE IIIA               33                 52
  STAGE IIIB               22                 40
  STAGE IIIC               12                 29
  STAGE IV                 13                 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
  22Q LOSS MUTATED     5  29  73  33
  22Q LOSS WILD-TYPE  17  61 122  86
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                5                 17
  T2               29                 61
  T3               73                122
  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   38 32 34 32
  22Q LOSS WILD-TYPE 91 86 50 57
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               38                 91
  N1               32                 86
  N2               34                 50
  N3               32                 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   130   6
  22Q LOSS WILD-TYPE 257  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    130    6
  22Q LOSS WILD-TYPE  257   24
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              130                257
  1                6                 24
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    49  93
  22Q LOSS WILD-TYPE 109 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     49   93
  22Q LOSS WILD-TYPE  109  185
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               49                109
  MALE                 93                185
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  22Q LOSS MUTATED                                      17
  22Q LOSS WILD-TYPE                                    54
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                       51
  22Q LOSS WILD-TYPE                                                    111
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                                  25
  22Q LOSS WILD-TYPE                                                                56
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  22Q LOSS MUTATED                                                 33
  22Q LOSS WILD-TYPE                                               45
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  22Q LOSS MUTATED                                                          8
  22Q LOSS WILD-TYPE                                                       13
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  22Q LOSS MUTATED                                                           2
  22Q LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  22Q LOSS MUTATED                                          6
  22Q LOSS WILD-TYPE                                        7
D79V8, multiclass
                                                                   clus
vv                                                                  22Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          51
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         6
                                                                   clus
vv                                                                  22Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           111
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[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"
D79V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     4 138
  22Q LOSS WILD-TYPE   2 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4  138
  22Q LOSS WILD-TYPE    2  292
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 4                  2
  YES              138                292
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED   109   8   8   6
  22Q LOSS WILD-TYPE 238  10  11  19
D79V10, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0              109                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                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           1    89
  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                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   89                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     1  98
  22Q LOSS WILD-TYPE   3 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   98
  22Q LOSS WILD-TYPE    3  215
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               98                215
[1] 2 2
[1] FALSE

Clustering(80) Variable = XP LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    38  16
  XP LOSS WILD-TYPE 216 134
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               54               350 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               16               134 
$`XP LOSS MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-8291 TCGA-BR-8297 
       19.56         9.44        18.35        19.33        16.31         7.40 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4CQ 
       19.50        13.08        15.81         9.86        13.87        22.26 
TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 
       13.64         0.07         0.13        11.31        12.20        20.02 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-5579 
       29.98        47.05        19.07         7.07        15.02        11.93 
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 
        9.76        15.65         7.40        13.58         5.52        12.10 
TCGA-HU-A4GD TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       22.75        12.30        21.21         3.39        18.38         5.19 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-R5-A7O7 TCGA-VQ-A8PC TCGA-VQ-A8PS TCGA-VQ-A8PU 
        6.44         6.74        45.67        46.26        13.35        27.35 
TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       52.24        64.18        22.09        40.08        32.94        17.13 

$`XP LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        30.90         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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        12.76        18.71        17.49        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8363 
       12.95         2.66         2.20        15.58         6.18         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        19.17        14.79         0.26        15.85 
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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        0.49        11.54        16.44        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56         7.53         6.08         1.48        13.41        13.51 
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        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         3.42         9.34        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        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-4455 
        7.99         8.05        54.08         4.01        14.01        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 
       21.99         0.00         9.01        18.97        12.00        22.98 
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-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        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        12.36        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        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       13.71        11.24        11.44         2.96         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62         7.99        16.24        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-A8CX TCGA-HF-A5NB 
       17.06        59.54         5.03         0.56         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        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         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ 
        8.88         8.81        27.42         3.45        18.81         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       13.08         1.41        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       37.64         3.72        19.73         9.86        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         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        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       32.48         7.73        28.96        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        26.24        64.57        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       36.69        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       22.68         1.71        36.16         7.36         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 
       29.98        54.12        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.07              0.00 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            64.18            122.30 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           15.120            12.605 
[1] "0.1 - 64.2 (15.1)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1.5"
D80V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED         1        1        6        3         4         9
  XP LOSS WILD-TYPE       2       13       35       28        34        46
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED           0         17          3          7        3
  XP LOSS WILD-TYPE         4         68         59         34       43
D80V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 1                13
  STAGE IB                 6                35
  STAGE II                 3                28
  STAGE IIA                4                34
  STAGE IIB                9                46
  STAGE III                0                 4
  STAGE IIIA              17                68
  STAGE IIIB               3                59
  STAGE IIIC               7                34
  STAGE IV                 3                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
  XP LOSS MUTATED     3  13  26  13
  XP LOSS WILD-TYPE  19  77 169 106
D80V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               3                19
  T2              13                77
  T3              26               169
  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 LOSS MUTATED    15  17  13   9
  XP LOSS WILD-TYPE 114 101  71  80
D80V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              15               114
  N1              17               101
  N2              13                71
  N3               9                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"
D80V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    53   2
  XP LOSS WILD-TYPE 334  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     53    2
  XP LOSS WILD-TYPE  334   28
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              53               334
  1               2                28
[1] 2 2
[1] FALSE
D80V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    14  42
  XP LOSS WILD-TYPE 144 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     14   42
  XP LOSS WILD-TYPE  144  236
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              14               144
  MALE                42               236
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  XP LOSS MUTATED                                       7
  XP LOSS WILD-TYPE                                    64
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XP LOSS MUTATED                                                       19
  XP LOSS WILD-TYPE                                                    143
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XP LOSS MUTATED                                                                   6
  XP LOSS WILD-TYPE                                                                75
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  XP LOSS MUTATED                                                 18
  XP LOSS WILD-TYPE                                               60
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  XP LOSS MUTATED                                                          2
  XP LOSS WILD-TYPE                                                       19
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  XP LOSS MUTATED                                                           1
  XP LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  XP LOSS MUTATED                                          3
  XP LOSS WILD-TYPE                                       10
D80V8, multiclass
                                                                   clus
vv                                                                  XP LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  XP LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          143
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                75
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 60
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         10
[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"
D80V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     1  55
  XP LOSS WILD-TYPE   5 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1   55
  XP LOSS WILD-TYPE    5  375
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                1                 5
  YES              55               375
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    45   4   0   2
  XP LOSS WILD-TYPE 302  14  19  23
D80V10, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              45               302
  R1               4                14
  R2               0                19
  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                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP LOSS MUTATED                                           0    39
  XP LOSS WILD-TYPE                                         1   235
D80V12, multiclass
                                           clus
vv                                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                                  10                78
  BLACK OR AFRICAN AMERICAN                               0                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  39               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"
D80V13, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     1  40
  XP LOSS WILD-TYPE   3 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1   40
  XP LOSS WILD-TYPE    3  273
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              40               273
[1] 2 2
[1] FALSE

Clustering(81) Variable = XQ LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    30  15
  XQ LOSS WILD-TYPE 224 135
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               45               359 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               15               135 
$`XQ LOSS MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-7197 TCGA-BR-8291 TCGA-BR-8361 
       19.56         9.44        18.35         9.21        16.31        19.50 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4QI 
       11.54        15.81        13.87        22.26         1.48        13.64 
TCGA-CD-8524 TCGA-CD-8535 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4443 TCGA-CG-4444 
        0.07         0.13        11.31        20.02        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6817 
       19.07         7.07        15.02        11.93        20.55        12.79 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A74A TCGA-FP-8211 
       12.33        18.21        11.31         9.76         7.40        13.58 
TCGA-FP-A4BF TCGA-HU-8604 TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RI 
        5.52        12.10        12.30        21.21         3.39        18.38 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-VQ-A8E0 TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91Q 
        6.44         6.74        18.48        13.35        27.35        20.81 
TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6D 
       22.09        32.94        17.13 

$`XQ LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        30.90         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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        12.76        18.71        17.49        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95         2.66         2.20        15.58         7.40         6.18 
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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        6.28         7.53         0.49        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
        8.22        10.68        12.56         7.53         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        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 
       12.82         0.66        19.36        13.51         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        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         3.42         9.34        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20         0.10        12.62         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-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        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-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.36        12.66        19.13        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-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        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-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.99        16.24        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-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.03         0.56         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
        5.92        14.27        12.59        14.17        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        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         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL 
        8.81        27.42         3.45        18.81         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       13.08         1.41        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         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-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       22.19         2.50        12.79         2.70        17.85         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        26.24        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       22.68         1.71        36.16         7.36         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       52.24         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        64.18        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        40.08        28.41        29.98        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.00 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            47.05            122.30 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            13.64             12.79 
[1] "0.1 - 47.0 (13.6)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         1        1        4        4         3         6
  XQ LOSS WILD-TYPE       2       13       37       27        35        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         4         70         59         36       42
D81V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  1                 2
  STAGE IA                 1                13
  STAGE IB                 4                37
  STAGE II                 4                27
  STAGE IIA                3                35
  STAGE IIB                6                49
  STAGE III                0                 4
  STAGE IIIA              15                70
  STAGE IIIB               3                59
  STAGE IIIC               5                36
  STAGE IV                 4                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
  XQ LOSS MUTATED     3  11  23  10
  XQ LOSS WILD-TYPE  19  79 172 109
D81V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               3                19
  T2              11                79
  T3              23               172
  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
  XQ LOSS MUTATED    13  12  12   9
  XQ LOSS WILD-TYPE 116 106  72  80
D81V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              13               116
  N1              12               106
  N2              12                72
  N3               9                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"
D81V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    46   1
  XQ LOSS WILD-TYPE 341  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     46    1
  XQ LOSS WILD-TYPE  341   29
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              46               341
  1               1                29
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    10  38
  XQ LOSS WILD-TYPE 148 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     10   38
  XQ LOSS WILD-TYPE  148  240
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              10               148
  MALE                38               240
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  XQ LOSS MUTATED                                       7
  XQ LOSS WILD-TYPE                                    64
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                       18
  XQ LOSS WILD-TYPE                                                    144
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                                   7
  XQ LOSS WILD-TYPE                                                                74
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  XQ LOSS MUTATED                                                 10
  XQ LOSS WILD-TYPE                                               68
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  XQ LOSS MUTATED                                                          3
  XQ LOSS WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  XQ LOSS MUTATED                                                           1
  XQ LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  XQ LOSS MUTATED                                          2
  XQ LOSS WILD-TYPE                                       11
D81V8, multiclass
                                                                   clus
vv                                                                  XQ LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  XQ LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          144
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                74
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 68
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         11
[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"
D81V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  46
  XQ LOSS WILD-TYPE   4 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   46
  XQ LOSS WILD-TYPE    4  384
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                2                 4
  YES              46               384
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    38   5   0   2
  XQ LOSS WILD-TYPE 309  13  19  23
D81V10, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              38               309
  R1               5                13
  R2               0                19
  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                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           0    31
  XQ LOSS WILD-TYPE                                         1   243
D81V12, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                                   7                81
  BLACK OR AFRICAN AMERICAN                               1                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  31               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"
D81V13, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  34
  XQ LOSS WILD-TYPE   4 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   34
  XQ LOSS WILD-TYPE    4  279
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              34               279
[1] 2 2
[1] FALSE
